5.7. 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.
5.7.1. Classes¶
-
class
MDAnalysis.coordinates.LAMMPS.
Timestep
(arg, **kwargs)[source]¶ LAMMPS trajectory time step
-
copy_slice
(sel)[source]¶ 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()
andMDAnalysis.Writer()
-
Writer
(filename, **kwargs)[source]¶ 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 isNone
, in which case step and delta are used.- remarks
string that is stored in the DCD header [XXX – max length?]
Returns: 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)[source]¶ Populate a TimeseriesCollection object with timeseries computed from the trajectory
Arguments: - timeseries
- 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')[source]¶ 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_trajectory
()¶ Specific implementation of trajectory closing.
-
convert_dimensions_to_unitcell
(ts, _ts_order=[0, 2, 5, 4, 3, 1])[source]¶ Read dimensions from timestep ts and return appropriate native unitcell.
See also
-
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 <= maxArguments: - 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 aUniverse
or aTimestep
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)[source]¶ 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 genericException
if wrong number of atoms supplied andNoDataError
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()
andMDAnalysis.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.
-