Merge pull request #3 from akohlmey/imd-v3-updates
Imd v3 Integration updates
This commit is contained in:
Oliver Beckstein
@ -579,6 +579,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
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endif()
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endforeach()
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# settings for misc packages and styles
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if(PKG_MISC)
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option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
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mark_as_advanced(LAMMPS_ASYNC_IMD)
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if(LAMMPS_ASYNC_IMD)
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target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
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message(STATUS "Using IMD in asynchronous mode")
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endif()
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endif()
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# optionally enable building script wrappers using swig
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option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
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if(WITH_SWIG)
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@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
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* :ref:`LEPTON <lepton>`
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* :ref:`MACHDYN <machdyn>`
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* :ref:`MDI <mdi>`
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* :ref:`MISC <misc>`
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* :ref:`ML-HDNNP <ml-hdnnp>`
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* :ref:`ML-IAP <mliap>`
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* :ref:`ML-PACE <ml-pace>`
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@ -2019,7 +2020,7 @@ TBB and MKL.
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.. _mdi:
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MDI package
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-----------------------------
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-----------
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.. tabs::
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@ -2046,6 +2047,37 @@ MDI package
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----------
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.. _misc:
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MISC package
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------------
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The :doc:`fix imd <fix_imd>` style in this package can be run either
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synchronously (communication with IMD clients is done in the main
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process) or asynchronously (the fix spawns a separate thread that can
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communicate with IMD clients concurrently to the LAMMPS execution).
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.. tabs::
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.. tab:: CMake build
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.. code-block:: bash
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-D LAMMPS_ASYNC_IMD=value # Run IMD server asynchronously
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# value = no (default) or yes
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.. tab:: Traditional make
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To enable asynchronous mode the ``-DLAMMPS_ASYNC_IMD`` define
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needs to be added to the ``LMP_INC`` variable in the
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``Makefile.machine`` you are using. For example:
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.. code-block:: make
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LMP_INC = -DLAMMPS_ASYNC_IMD -DLAMMPS_MEMALIGN=64
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----------
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.. _molfile:
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MOLFILE package
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@ -49,6 +49,7 @@ packages:
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* :ref:`LEPTON <lepton>`
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* :ref:`MACHDYN <machdyn>`
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* :ref:`MDI <mdi>`
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* :ref:`MISC <misc>`
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* :ref:`ML-HDNNP <ml-hdnnp>`
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* :ref:`ML-IAP <mliap>`
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* :ref:`ML-PACE <ml-pace>`
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@ -27,8 +27,13 @@ Syntax
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off = LAMMPS waits to be connected to an IMD client before continuing (default)
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on = LAMMPS listens for an IMD client, but continues with the run
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*version* arg = *2* or *3*
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2 = use IMD version 2 (default)
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3 = use IMD version 3. The subsequent keywords are only supported for version 3.
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2 = use IMD protocol version 2 (default)
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3 = use IMD protocol version 3.
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The following keywords are only supported for IMD protocol version 3.
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.. parsed-literal::
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*time* arg = *on* or *off*
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off = simulation time is not transmitted (default)
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on = simulation time is transmitted.
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@ -58,19 +63,19 @@ Description
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This fix implements the "Interactive MD" (IMD) protocol which allows
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realtime visualization and manipulation of MD simulations through the
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IMD protocol, as initially implemented in VMD and NAMD. Specifically
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it allows LAMMPS to connect an IMD client, for example the `VMD visualization program <VMD_>`_
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(currently only supports IMDv2) or the
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`Python IMDClient <IMDClient_>`_ (supports both IMDv2 and IMDv3),
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so that it can monitor the progress of the
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simulation and interactively apply forces to selected atoms.
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IMD protocol, as initially implemented in VMD and NAMD. Specifically it
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allows LAMMPS to connect an IMD client, for example the `VMD
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visualization program <VMD_>`_ (currently only supports IMDv2) or the
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`Python IMDClient <IMDClient_>`_ (supports both IMDv2 and IMDv3), so
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that it can monitor the progress of the simulation and interactively
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apply forces to selected atoms.
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If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD (-DCMAKE_CXX_FLAGS="-DLAMMPS_ASYNC_IMD" in CMake),
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then fix imd will use POSIX threads to spawn a IMD communication
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thread on MPI rank 0 in order to offload data reading and writing
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from the main execution thread and potentially lower the inferred
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latencies for slow communication links. This feature has only been
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tested under linux.
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If LAMMPS is compiled with the pre-processor flag
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:ref:`-DLAMMPS_ASYNC_IMD <misc>` then fix imd will use POSIX threads to
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spawn an IMD communication thread on MPI rank 0 in order to offload data
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exchange with the IMD client from the main execution thread and
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potentially lower the inferred latencies for slow communication
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links. This feature has only been tested under linux.
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The source code for this fix includes code developed by the Theoretical
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and Computational Biophysics Group in the Beckman Institute for Advanced
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@ -115,12 +120,14 @@ with different units or as a measure to tweak the forces generated by
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the manipulation of the IMD client, this option allows to make
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adjustments.
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In `IMDv3 <IMDv3_>`_, the protocol has been extended to allow for the transmission
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of simulation time, box dimensions, atomic coordinates, velocities, and
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forces. The *version* keyword allows to select the version of the
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protocol to be used. The *time*, *box*, *coordinates*, *velocities*,
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and *forces* keywords allow to select which data is transmitted to the
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IMD client. The default is to transmit all data.
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.. versionadded:: TBD
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In `IMDv3 <IMDv3_>`_, the IMD protocol has been extended to allow for
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the transmission of simulation time, box dimensions, atomic coordinates,
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velocities, and forces. The *version* keyword allows to select the
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version of the protocol to be used. The *time*, *box*, *coordinates*,
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*velocities*, and *forces* keywords allow to select which data is
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transmitted to the IMD client. The default is to transmit all data.
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To connect VMD to a listening LAMMPS simulation on the same machine
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with fix imd enabled, one needs to start VMD and load a coordinate or
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@ -179,14 +186,14 @@ This fix is part of the MISC package. It is only enabled if LAMMPS was
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built with that package. See the :doc:`Build package <Build_package>`
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page for more info.
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When used in combination with VMD, a topology or coordinate file has
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to be loaded, which matches (in number and ordering of atoms) the
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group the fix is applied to. The fix internally sorts atom IDs by
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ascending integer value; in VMD (and thus the IMD protocol) those will
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be assigned 0-based consecutive index numbers.
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When used in combination with VMD, a topology or coordinate file has to
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be loaded, which matches (in number and ordering of atoms) the group the
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fix is applied to. The fix internally sorts atom IDs by ascending
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integer value; in VMD (and thus the IMD protocol) those will be assigned
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0-based consecutive index numbers.
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When using multiple active IMD connections at the same time, each
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needs to use a different port number.
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fix instance needs to use a different port number.
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Related commands
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""""""""""""""""
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@ -454,29 +454,31 @@ struct commdata {
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MPI_Datatype MPI_CommData;
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/***************************************************************
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* create class and parse arguments in LAMMPS script. Syntax:
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* fix ID group-ID imd <imd_port> [trate <imd_trate>] [version (2|3)] [unwrap (on|off)] [fscale <imd_fscale>] [time (on|off)] [box (on|off)] [coordinates (on|off)] [velocities (on|off)] [forces (on|off)]
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* create class and parse arguments in LAMMPS script.
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***************************************************************/
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FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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Fix(lmp, narg, arg), localsock(nullptr), clientsock(nullptr), coord_data(nullptr),
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vel_data(nullptr), force_data(nullptr), idmap(nullptr), rev_idmap(nullptr),
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recv_force_buf(nullptr), imdsinfo(nullptr), msgdata(nullptr)
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{
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if (narg < 4)
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error->all(FLERR,"Illegal fix imd command");
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if (narg < 4) utils::missing_cmd_args(FLERR, "fix imd", error);
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imd_port = utils::inumeric(FLERR,arg[3],false,lmp);
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if (imd_port < 1024)
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error->all(FLERR,"Illegal fix imd parameter: port < 1024");
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if (imd_port < 1024) error->all(FLERR,"Illegal fix imd parameter: port < 1024");
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/* default values for optional flags */
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imd_version = 2;
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imd_version = 2;
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unwrap_flag = 0;
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nowait_flag = 0;
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connect_msg = 1;
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imd_fscale = 1.0;
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imd_trate = 1;
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/* IMDv3-only flags. Aren't stored as class attributes since they're converted into IMDSessionInfo */
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// IMDv3-only flags.
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// Aren't stored as class attributes since they're converted into IMDSessionInfo
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int time_flag = 1;
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int box_flag = 1;
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int coord_flag = 1;
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@ -507,17 +509,17 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
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} else if (0 == strcmp(arg[iarg], "forces")) {
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force_flag = utils::logical(FLERR, arg[iarg+1], false, lmp);
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} else {
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error->all(FLERR,"Unknown fix imd parameter");
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error->all(FLERR,"Unknown fix imd parameter: {}", arg[iarg]);
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}
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++iarg; ++iarg;
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}
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/* sanity check on parameters */
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if (imd_trate < 1)
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error->all(FLERR,"Illegal fix imd parameter. trate < 1.");
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error->all(FLERR,"Illegal fix imd trate parameter. trate < 1.");
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if (imd_version != 2 && imd_version != 3)
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error->all(FLERR,"Illegal fix imd parameter. version != 2 or 3.");
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error->all(FLERR,"Illegal fix imd version parameter: version != 2 or 3.");
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imdsinfo = new IMDSessionInfo;
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@ -553,19 +555,11 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
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MPI_Comm_rank(world,&me);
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/* initialize various imd state variables. */
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clientsock = nullptr;
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localsock = nullptr;
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nlevels_respa = 0;
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imd_inactive = 0;
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imd_terminate = 0;
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imd_forces = 0;
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recv_force_buf = nullptr;
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maxbuf = 0;
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coord_data = nullptr;
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vel_data = nullptr;
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force_data = nullptr;
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idmap = nullptr;
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rev_idmap = nullptr;
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if (imd_version == 3) {
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msglen = 0;
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@ -673,8 +667,8 @@ FixIMD::~FixIMD()
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imdsock_destroy(clientsock);
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imdsock_shutdown(localsock);
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imdsock_destroy(localsock);
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clientsock=nullptr;
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localsock=nullptr;
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clientsock = nullptr;
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localsock = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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