imd sample integration

package/MDAnalysis/coordinates/IMD.py

@@ -0,0 +1,289 @@
+"""
+
+Example: Streaming an IMD v3 trajectory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To stream a trajectory from GROMACS or another simulation engine that supports 
+IMD v3, ensure that the simulation engine is running and waiting for an IMD connection.
+
+For example, in GROMACS, you can use ``gmx mdrun`` with the ``-imdwait`` flag
+to ensure that GROMACS will wait for a client before starting the simulation.
+In GROMACS, you will know that the simulation is ready and waiting for the
+MDAnalysis IMDReader client when this line is printed to the terminal:
+
+.. code-block:: none
+
+    IMD: Will wait until I have a connection and IMD_GO orders.
+
+Once the simulation is ready for a client connection, setup your :class:`Universe`
+like this: ::
+
+    import MDAnalysis as mda
+    # Pass host and port of the listening GROMACS simulation
+    # server as the trajectory argument
+    u = mda.Universe("topology.tpr", "localhost:8888")
+
+Classes
+^^^^^^^
+
+.. autoclass:: IMDReader
+   :members:
+   :inherited-members:
+
+"""
+
+import queue
+from MDAnalysis.coordinates.base import (
+    ReaderBase,
+    FrameIteratorIndices,
+    FrameIteratorAll,
+    FrameIteratorSliced,
+)
+from MDAnalysis.coordinates import core
+from MDAnalysis.lib.util import store_init_arguments
+
+import imdclient
+from imdclient.utils import parse_host_port
+import numpy as np
+import logging
+import warnings
+from typing import Optional
+import numbers
+
+logger = logging.getLogger("imdclient.IMDClient")
+
+
+class IMDReader(ReaderBase):
+    """
+    Reader for IMD protocol packets.
+    """
+
+    format = "IMD"
+
+    @store_init_arguments
+    def __init__(
+        self,
+        filename,
+        convert_units=True,
+        n_atoms=None,
+        **kwargs,
+    ):
+        """
+        Parameters
+        ----------
+        filename : a string of the form "host:port" where host is the hostname
+            or IP address of the listening GROMACS server and port
+            is the port number.
+        n_atoms : int (optional)
+            number of atoms in the system. defaults to number of atoms
+            in the topology. don't set this unless you know what you're doing.
+        """
+        self._init_scope = True
+        self._reopen_called = False
+
+        super(IMDReader, self).__init__(filename, **kwargs)
+
+        logger.debug("IMDReader initializing")
+
+        if n_atoms is None:
+            raise ValueError("IMDReader: n_atoms must be specified")
+        self.n_atoms = n_atoms
+
+        host, port = parse_host_port(filename)
+
+        # This starts the simulation
+        self._imdclient = imdclient.IMDClient(host, port, n_atoms, **kwargs)
+
+        imdsinfo = self._imdclient.get_imdsessioninfo()
+        # NOTE: after testing phase, fail out on IMDv2
+
+        self.ts = self._Timestep(
+            self.n_atoms,
+            positions=imdsinfo.positions,
+            velocities=imdsinfo.velocities,
+            forces=imdsinfo.forces,
+            **self._ts_kwargs,
+        )
+
+        self._frame = -1
+
+        try:
+            self._read_next_timestep()
+        except StopIteration:
+            raise RuntimeError("IMDReader: No data found in stream")
+
+    def _read_next_timestep(self):
+        # No rewinding- to both load the first frame after  __init__
+        # and access it again during iteration, we need to store first ts in mem
+        if not self._init_scope and self._frame == -1:
+            self._frame += 1
+            # can't simply return the same ts again- transformations would be applied twice
+            # instead, return the pre-transformed copy
+            return self._first_ts
+
+        return self._read_frame(self._frame + 1)
+
+    def _read_frame(self, frame):
+
+        try:
+            imdf = self._imdclient.get_imdframe()
+        except EOFError:
+            # Not strictly necessary, but for clarity
+            raise StopIteration
+
+        self._frame = frame
+        self._load_imdframe_into_ts(imdf)
+
+        if self._init_scope:
+            self._first_ts = self.ts.copy()
+            self._init_scope = False
+
+        logger.debug(f"IMDReader: Loaded frame {self._frame}")
+        return self.ts
+
+    def _load_imdframe_into_ts(self, imdf):
+        self.ts.frame = self._frame
+        if imdf.time is not None:
+            self.ts.time = imdf.time
+            # NOTE: timestep.pyx "dt" method is suspicious bc it uses "new" keyword for a float
+            self.ts.data["dt"] = imdf.dt
+        if imdf.energies is not None:
+            self.ts.data.update(imdf.energies)
+        if imdf.box is not None:
+            self.ts.dimensions = core.triclinic_box(*imdf.box)
+        if imdf.positions is not None:
+            # must call copy because reference is expected to reset
+            # see 'test_frame_collect_all_same' in MDAnalysisTests.coordinates.base
+            self.ts.positions = imdf.positions
+        if imdf.velocities is not None:
+            self.ts.velocities = imdf.velocities
+        if imdf.forces is not None:
+            self.ts.forces = imdf.forces
+
+    @property
+    def n_frames(self):
+        """Changes as stream is processed unlike other readers"""
+        raise RuntimeError("IMDReader: n_frames is unknown")
+
+    def next(self):
+        """Don't rewind after iteration. When _reopen() is called,
+        an error will be raised
+        """
+        try:
+            ts = self._read_next_timestep()
+        except (EOFError, IOError):
+            # Don't rewind here like we normally would
+            raise StopIteration from None
+        else:
+            for auxname, reader in self._auxs.items():
+                ts = self._auxs[auxname].update_ts(ts)
+
+            ts = self._apply_transformations(ts)
+
+        return ts
+
+    def rewind(self):
+        """Raise error on rewind"""
+        raise RuntimeError("IMDReader: Stream-based readers can't be rewound")
+
+    @staticmethod
+    def _format_hint(thing):
+        try:
+            parse_host_port(thing)
+        except:
+            return False
+        return True
+
+    def close(self):
+        """Gracefully shut down the reader. Stops the producer thread."""
+        logger.debug("IMDReader close() called")
+        self._imdclient.stop()
+        # NOTE: removeme after testing
+        logger.debug("IMDReader shut down gracefully.")
+
+    # Incompatible methods
+    def copy(self):
+        raise NotImplementedError("IMDReader does not support copying")
+
+    def _reopen(self):
+        if self._reopen_called:
+            raise RuntimeError("IMDReader: Cannot reopen IMD stream")
+        self._frame = -1
+        self._reopen_called = True
+
+    def __getitem__(self, frame):
+        """This method from ProtoReader must be overridden
+        to prevent slicing that doesn't make sense in a stream.
+        """
+        raise RuntimeError("IMDReader: Trajectory can only be read in for loop")
+
+    def check_slice_indices(self, start, stop, step):
+        """Check frame indices are valid and clip to fit trajectory.
+
+        The usage follows standard Python conventions for :func:`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 : tuple (int, int, int)
+          Integers representing the slice
+
+        Warning
+        -------
+        The returned values `start`, `stop` and `step` give the expected result
+        when passed in :func:`range` but gives unexpected behavior when passed
+        in a :class:`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 :meth:`check_slice_indices` to :func:`range` ::
+
+          range(start, stop, step)
+
+        and using them as the indices to randomly seek to. On the other hand,
+        in :class:`MDAnalysis.analysis.base.AnalysisBase` the values returned
+        by :meth:`check_slice_indices` are used to splice the trajectory by
+        creating a :class:`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)]  # []
+
+        """
+        if start is not None:
+            raise ValueError(
+                "IMDReader: Cannot slice a stream, 'start' must be None"
+            )
+        if stop is not None:
+            raise ValueError(
+                "IMDReader: Cannot slice a stream, 'stop' must be None"
+            )
+        if step is not None:
+            if isinstance(step, numbers.Integral):
+                if step != 1:
+                    raise ValueError(
+                        "IMDReader: Cannot slice a stream, 'step' must be None or 1"
+                    )
+
+        return start, stop, step
+
+    def __getstate__(self):
+        raise NotImplementedError("IMDReader does not support pickling")
+
+    def __setstate__(self, state: object):
+        raise NotImplementedError("IMDReader does not support pickling")

package/MDAnalysis/coordinates/__init__.py

@@ -757,7 +757,7 @@ class can choose an appropriate reader automatically.
    raw :class:`~MDAnalysis.coordinates.Timestep` objects.
 
 """
-__all__ = ['reader', 'writer', 'timestep']
+__all__ = ["reader", "writer", "timestep"]
 
 from . import base
 from . import timestep
@@ -770,6 +770,7 @@ class can choose an appropriate reader automatically.
 from . import DMS
 from . import GMS
 from . import GRO
+from . import IMD
 from . import INPCRD
 from . import LAMMPS
 from . import MOL2

package/pyproject.toml

@@ -43,6 +43,7 @@ dependencies = [
     'waterdynamics',
     'pathsimanalysis',
     'mdahole2',
+    "imdclient @ git+https://github.com/ljwoods2/imdclient.git@main",
 ]
 keywords = [
     "python", "science", "chemistry", "biophysics", "molecular-dynamics",