imdclient 0.1.2__tar.gz → 0.1.4__tar.gz

imdclient-0.1.4/LICENSE

@@ -0,0 +1,5 @@
+Copyright 2024 Lawson Woods
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

imdclient-0.1.4/PKG-INFO

@@ -0,0 +1,132 @@
+Metadata-Version: 2.1
+Name: imdclient
+Version: 0.1.4
+Summary: Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
+Author-email: Lawson <ljwoods2@asu.edu>
+Maintainer-email: Lawson <ljwoods2@asu.edu>
+License: Copyright 2024 Lawson Woods
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+Keywords: molecular simulations
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: MDAnalysis>=2.7.0
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-xdist>=2.5; extra == "test"
+Requires-Dist: pytest-cov>=3.0; extra == "test"
+Requires-Dist: MDAnalysisTests>=2.7.0; extra == "test"
+Requires-Dist: docker-py; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+
+IMDClient
+==============================
+[//]: # (Badges)
+
+| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
+| :----------------- | :------- |
+| **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
+| **Community**      | [![License: MIT][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+
+[badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
+[badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
+[badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
+[badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
+[badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
+[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA
+[badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
+[url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
+[url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
+[url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
+[url_latest_release]: https://github.com/becksteinlab/imdclient/releases
+[url_license]: https://opensource.org/license/mit
+[url_mda]: https://www.mdanalysis.org
+
+Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
+
+IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
+
+### Installation
+
+IMDClient is available via PyPi and can be installed with pip:
+```bash
+pip install imdclient
+```
+
+To build IMDClient from source,
+we highly recommend using virtual environments.
+If possible, we strongly recommend that you use
+[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
+Below we provide instructions both for `conda` and
+for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```
+conda create --name imdclient
+conda activate imdclient
+```
+
+<!-- Install the development and documentation dependencies:
+
+```
+conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
+conda env update --name imdreader --file docs/requirements.yaml
+``` -->
+
+Build this package from source:
+
+```
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```
+pip install ".[test,doc]"
+```
+
+### Copyright
+
+The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
+and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
+
+Copyright (c) 2024, Lawson
+
+
+#### Acknowledgements
+ 
+Project based on the 
+[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
+<!-- Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using IMDReader in published work. --> 

{imdclient-0.1.2 → imdclient-0.1.4}/README.md

@@ -5,28 +5,33 @@ IMDClient
 | **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
 | :----------------- | :------- |
 | **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
-| **Community**      | [![License: GPL v3][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+| **Community**      | [![License: MIT][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
 
 [badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
 [badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
 [badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
 [badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
-[badge_license]: https://img.shields.io/badge/License-GPLv3-blue.svg
+[badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
 [badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
 [badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
 [url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
 [url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
 [url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
 [url_latest_release]: https://github.com/becksteinlab/imdclient/releases
-[url_license]: https://www.gnu.org/licenses/gpl-3.0
+[url_license]: https://opensource.org/license/mit
 [url_mda]: https://www.mdanalysis.org
 
-Receiver for IMDv3 protocol from simulation engines like Gromacs, LAMMPS, and NAMD.
+Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
 
 IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
 
 ### Installation
 
+IMDClient is available via PyPi and can be installed with pip:
+```bash
+pip install imdclient
+```
+
 To build IMDClient from source,
 we highly recommend using virtual environments.
 If possible, we strongly recommend that you use
@@ -88,7 +93,7 @@ pip install ".[test,doc]"
 ### Copyright
 
 The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
-and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
+and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
 
 Copyright (c) 2024, Lawson
 

imdclient-0.1.2/imdclient/IMDREADER.py → imdclient-0.1.4/imdclient/IMD.py

@@ -50,6 +50,7 @@ class IMDReader(StreamReaderBase):
     ):
         super(IMDReader, self).__init__(filename, **kwargs)
 
+        self._imdclient = None
         logger.debug("IMDReader initializing")
 
         if n_atoms is None:
@@ -83,9 +84,8 @@ class IMDReader(StreamReaderBase):
 
         try:
             imdf = self._imdclient.get_imdframe()
-        except EOFError:
-            # Not strictly necessary, but for clarity
-            raise StopIteration
+        except EOFError as e:
+            raise e
 
         self._frame = frame
         self._load_imdframe_into_ts(imdf)
@@ -126,6 +126,7 @@ class IMDReader(StreamReaderBase):
     def close(self):
         """Gracefully shut down the reader. Stops the producer thread."""
         logger.debug("IMDReader close() called")
-        self._imdclient.stop()
+        if self._imdclient is not None:
+            self._imdclient.stop()
         # NOTE: removeme after testing
         logger.debug("IMDReader shut down gracefully.")

{imdclient-0.1.2 → imdclient-0.1.4}/imdclient/IMDClient.py

@@ -25,6 +25,7 @@ import time
 import numpy as np
 from typing import Union, Dict
 import signal
+import atexit
 
 logger = logging.getLogger(__name__)
 
@@ -42,7 +43,13 @@ class IMDClient:
     socket_bufsize : int, (optional)
         Size of the socket buffer in bytes. Default is to use the system default
     buffer_size : int (optional)
-        IMDFramebuffer will be filled with as many :class:`IMDFrame` fit in `buffer_size` [``10MB``]
+        IMDFramebuffer will be filled with as many :class:`IMDFrame` fit in `buffer_size` bytes [``10MB``]
+    timeout : int, optional
+        Timeout for the socket in seconds [``5``]
+    continue_after_disconnect : bool, optional [``None``]
+        If True, the client will attempt to change the simulation engine's waiting behavior to
+        non-blocking after the client disconnects. If False, the client will attempt to change it
+        to blocking. If None, the client will not attempt to change the simulation engine's behavior.
     **kwargs : dict (optional)
         Additional keyword arguments to pass to the :class:`BaseIMDProducer` and :class:`IMDFrameBuffer`
     """
@@ -54,6 +61,7 @@ class IMDClient:
         n_atoms,
         socket_bufsize=None,
         multithreaded=True,
+        continue_after_disconnect=None,
         **kwargs,
     ):
 
@@ -61,6 +69,7 @@ class IMDClient:
         self._conn = self._connect_to_server(host, port, socket_bufsize)
         self._imdsinfo = self._await_IMD_handshake()
         self._multithreaded = multithreaded
+        self._continue_after_disconnect = continue_after_disconnect
 
         if self._multithreaded:
             self._buf = IMDFrameBuffer(
@@ -68,8 +77,10 @@ class IMDClient:
                 n_atoms,
                 **kwargs,
             )
+            self._error_queue = queue.Queue()
         else:
             self._buf = None
+            self._error_queue = None
         if self._imdsinfo.version == 2:
             self._producer = IMDProducerV2(
                 self._conn,
@@ -77,6 +88,7 @@ class IMDClient:
                 self._imdsinfo,
                 n_atoms,
                 multithreaded,
+                self._error_queue,
                 **kwargs,
             )
         elif self._imdsinfo.version == 3:
@@ -86,23 +98,60 @@ class IMDClient:
                 self._imdsinfo,
                 n_atoms,
                 multithreaded,
+                self._error_queue,
                 **kwargs,
             )
 
         self._go()
 
         if self._multithreaded:
+            # Disconnect MUST occur. This covers typical cases (Python, IPython interpreter)
             signal.signal(signal.SIGINT, self.signal_handler)
+            signal.signal(signal.SIGTERM, self.signal_handler)
+
+            # Disconnect and socket shutdown MUST occur. This covers Jupyter use
+            # since in jupyter, the signal handler is reset to the default
+            # by pre- and post- hooks
+            # https://stackoverflow.com/questions/70841648/jupyter-reverts-signal-handler-to-default-when-running-next-cell
+            try:
+                import IPython
+            except ImportError:
+                has_ipython = False
+            else:
+                has_ipython = True
+
+            if has_ipython:
+                try:
+                    from IPython import get_ipython
+
+                    if get_ipython() is not None:
+                        kernel = get_ipython().kernel
+                        kernel.pre_handler_hook = lambda: None
+                        kernel.post_handler_hook = lambda: None
+                        logger.debug("Running in Jupyter")
+                except NameError:
+                    logger.debug("Running in non-jupyter IPython environment")
+
+            # Final case: error is raised outside of IMDClient code
+            logger.debug("Registering atexit")
+            atexit.register(self.stop)
+
             self._producer.start()
 
     def signal_handler(self, sig, frame):
         """Catch SIGINT to allow clean shutdown on CTRL+C
         This also ensures that main thread execution doesn't get stuck
         waiting in buf.pop_full_imdframe()"""
+        logger.debug("Intercepted signal")
         self.stop()
+        logger.debug("Shutdown success")
 
     def get_imdframe(self):
         """
+        Returns
+        -------
+        IMDFrame
+            The next frame from the IMD server
         Raises
         ------
         EOFError
@@ -116,6 +165,9 @@ class IMDClient:
                 # and doesn't need to be notified
                 self._disconnect()
                 self._stopped = True
+
+                if self._error_queue.qsize():
+                    raise EOFError(f"{self._error_queue.get()}")
                 raise EOFError
         else:
             try:
@@ -125,14 +177,23 @@ class IMDClient:
                 raise EOFError
 
     def get_imdsessioninfo(self):
+        """
+        Returns
+        -------
+        IMDSessionInfo
+            Information about the IMD session
+        """
         return self._imdsinfo
 
     def stop(self):
+        """
+        Stop the client and close the connection
+        """
         if self._multithreaded:
             if not self._stopped:
-                self._buf.notify_consumer_finished()
-                self._disconnect()
                 self._stopped = True
+                self._disconnect()
+                self._buf.notify_consumer_finished()
         else:
             self._disconnect()
 
@@ -239,6 +300,17 @@ class IMDClient:
         self._conn.sendall(go)
         logger.debug("IMDClient: Sent go packet to server")
 
+        if self._continue_after_disconnect is not None:
+            wait_behavior = (int)(not self._continue_after_disconnect)
+            wait_packet = create_header_bytes(
+                IMDHeaderType.IMD_WAIT, wait_behavior
+            )
+            self._conn.sendall(wait_packet)
+            logger.debug(
+                "IMDClient: Attempted to change wait behavior to %s", 
+                not self._continue_after_disconnect 
+            )
+
     def _disconnect(self):
         # MUST disconnect before stopping execution
         # if simulation already ended, this method will do nothing
@@ -254,6 +326,13 @@ class IMDClient:
         finally:
             self._conn.close()
 
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.stop()
+        return False
+
 
 class BaseIMDProducer(threading.Thread):
     """
@@ -269,11 +348,14 @@ class BaseIMDProducer(threading.Thread):
         Information about the IMD session
     n_atoms : int
         Number of atoms in the simulation
-    multithreaded : bool, optional
+    multithreaded : bool
         If True, socket interaction will occur in a separate thread &
         frames will be buffered. Single-threaded, blocking IMDClient
-        should only be used in testing [[``True``]]
-
+        should only be used in testing
+    error_queue: queue.Queue
+        Queue to hold errors produced by the producer thread
+    timeout : int, optional
+        Timeout for the socket in seconds [``5``]
     """
 
     def __init__(
@@ -282,7 +364,8 @@ class BaseIMDProducer(threading.Thread):
         buffer,
         sinfo,
         n_atoms,
-        multithreaded=True,
+        multithreaded,
+        error_queue,
         timeout=5,
         **kwargs,
     ):
@@ -291,6 +374,7 @@ class BaseIMDProducer(threading.Thread):
         self._imdsinfo = sinfo
         self._paused = False
 
+        self.error_queue = error_queue
         # Timeout for first frame should be longer
         # than rest of frames
         self._timeout = timeout
@@ -385,6 +469,7 @@ class BaseIMDProducer(threading.Thread):
             logger.debug("IMDProducer: Simulation ended normally, cleaning up")
         except Exception as e:
             logger.debug("IMDProducer: An unexpected error occurred: %s", e)
+            self.error_queue.put(e)
         finally:
             logger.debug("IMDProducer: Stopping run loop")
             # Tell consumer not to expect more frames to be added
@@ -400,9 +485,19 @@ class BaseIMDProducer(threading.Thread):
             )
         # Sometimes we do not care what the value is
         if expected_value is not None and header.length != expected_value:
-            raise RuntimeError(
-                f"IMDProducer: Expected header value {expected_value}, got {header.length}"
-            )
+            if expected_type in [
+                IMDHeaderType.IMD_FCOORDS,
+                IMDHeaderType.IMD_VELOCITIES,
+                IMDHeaderType.IMD_FORCES,
+            ]:
+                raise RuntimeError(
+                    f"IMDProducer: Expected n_atoms value {expected_value}, got {header.length}. "
+                    + "Ensure you are using the correct topology file."
+                )
+            else:
+                raise RuntimeError(
+                    f"IMDProducer: Expected header value {expected_value}, got {header.length}"
+                )
 
     def _get_header(self):
         self._read(self._header)
@@ -422,9 +517,18 @@ class BaseIMDProducer(threading.Thread):
 
 
 class IMDProducerV2(BaseIMDProducer):
-    def __init__(self, conn, buffer, sinfo, n_atoms, multithreaded, **kwargs):
+    def __init__(
+        self,
+        conn,
+        buffer,
+        sinfo,
+        n_atoms,
+        multithreaded,
+        error_queue,
+        **kwargs,
+    ):
         super(IMDProducerV2, self).__init__(
-            conn, buffer, sinfo, n_atoms, multithreaded, **kwargs
+            conn, buffer, sinfo, n_atoms, multithreaded, error_queue, **kwargs
         )
 
         self._energies = bytearray(IMDENERGYPACKETLENGTH)
@@ -517,6 +621,7 @@ class IMDProducerV3(BaseIMDProducer):
         sinfo,
         n_atoms,
         multithreaded,
+        error_queue,
         **kwargs,
     ):
         super(IMDProducerV3, self).__init__(
@@ -525,6 +630,7 @@ class IMDProducerV3(BaseIMDProducer):
             sinfo,
             n_atoms,
             multithreaded,
+            error_queue,
             **kwargs,
         )
         # The body of an x/v/f packet should contain
@@ -633,9 +739,6 @@ class IMDProducerV3(BaseIMDProducer):
                 ).reshape((self._n_atoms, 3)),
             )
 
-    def __del__(self):
-        logger.debug("IMDProducer: I am being deleted")
-
 
 class IMDFrameBuffer:
     """

{imdclient-0.1.2 → imdclient-0.1.4}/imdclient/IMDProtocol.py

@@ -34,6 +34,7 @@ class IMDHeaderType(Enum):
     IMD_BOX = 13
     IMD_VELOCITIES = 14
     IMD_FORCES = 15
+    IMD_WAIT = 16
 
 
 def parse_energy_bytes(data, endianness):

{imdclient-0.1.2 → imdclient-0.1.4}/imdclient/data/gromacs/md/gromacs_v3_nst1.mdp

@@ -1,5 +1,5 @@
 title                   = PRODUCTION IN NPT
-ld-seed                 = 1
+ld-seed			= 1
 ; Run parameters
 integrator              = md        ; leap-frog integrator
 nsteps                  = 100    ; 1 * 1000 = 1 ps
@@ -7,9 +7,9 @@ dt                      = 0.001     ; 1 fs
 ; Output control
 nstxout                 = 1      ; save coordinates every 1 fs
 nstvout                 = 1      ; save velocities every 1 fs
-nstfout                 = 1
+nstfout                 = 1      ; save forces every 1 fs
 nstenergy               = 1      ; save energies every 1 fs
-nstlog                  = 10      ; update log file every 1 ps
+nstlog                  = 10     
 ; Center of mass (COM) motion
 nstcomm                 = 10        ; remove COM motion every 10 steps
 comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 

imdclient-0.1.4/imdclient/data/gromacs/md/gromacs_v3_nst8.mdp

@@ -0,0 +1,58 @@
+title                   = PRODUCTION IN NPT
+ld-seed                 = 1
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 100    ; 1 * 1000 = 1 ps
+dt                      = 0.001     ; 1 fs
+; Output control
+nstxout                 = 8      ; save coordinates every 1 fs
+nstvout                 = 8      ; save velocities every 1 fs
+nstfout                 = 8
+nstenergy               = 8      ; save energies every 1 fs
+nstlog                  = 10      ; update log file every 1 ps
+; Center of mass (COM) motion
+nstcomm                 = 10        ; remove COM motion every 10 steps
+comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
+; Bond parameters
+continuation            = yes       ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints
+constraints             = all-bonds ; all bonds lengths are constrained
+lincs_iter              = 1         ; accuracy of LINCS
+lincs_order             = 4         ; also related to accuracy
+; Nonbonded settings
+cutoff-scheme           = Verlet    ; Buffered neighbor searching
+ns_type                 = grid      ; search neighboring grid cells
+nstlist                 = 10        ; 10 fs, largely irrelevant with Verlet
+rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
+rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
+DispCorr                = EnerPres  ; account for cut-off vdW scheme
+; Electrostatics
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+; we define separate thermostats for the solute and solvent (need to adapt)
+; see default groups defined by Gromacs for your system or define your own (make_ndx)
+tc-grps                 = Protein  SOL      ; the separate groups for the thermostats
+tau-t                   = 1.0      1.0      ; time constants for thermostats (ps)
+ref-t                   = 300      300      ; reference temperature for thermostats (K)
+; Pressure coupling is off
+pcoupl                  = Parrinello-Rahman ; good for production, after equilibration
+tau-p                   = 2.0               ; time constant for barostat (ps)
+compressibility         = 4.5e-5            ; compressibility (1/bar) set to water at ~300K
+ref-p                   = 1.0               ; reference pressure for barostat (bar)
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no
+IMD-group               = System
+IMD-nst                 = 8
+IMD-version             = 3
+IMD-time                = yes
+IMD-box                 = yes
+IMD-coords              = yes
+IMD-unwrap              = no
+IMD-vels                = yes
+IMD-forces              = yes
+IMD-energies            = no

imdclient-0.1.2/imdclient/data/lammps/md/lammps_v3.in → imdclient-0.1.4/imdclient/data/lammps/md/lammps_v3_nst_1.in

@@ -52,8 +52,8 @@ velocity all create 300 102939 dist gaussian mom yes rot yes
 fix 1 all nve 
 
 # Create source of truth trajectory
-# dump h5md1 all h5md 1 lammps_trj.h5md position velocity force box yes
-# dump_modify h5md1 unwrap no
+dump h5md1 all h5md 1 lammps_trj.h5md position velocity force box yes
+dump_modify h5md1 unwrap no
 
 ## IMD settings
 # https://docs.lammps.org/fix_imd.html
@@ -63,7 +63,7 @@ fix 2 all imd 8888 version 3 unwrap off nowait off
 run 100
 
 # Stop dumping information to the dump file.
-# undump h5md1 
+undump h5md1 
 
 # Unfix the NVE. Additional lines if any will assume that this fix is off.
 unfix 1