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ljwoods2
2024-12-17 14:36:41 -07:00
parent 3d29991947
commit 2c9ad698ca
1 changed files with 34 additions and 2 deletions
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doc/src/fix_imd.rst
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@ -26,6 +26,24 @@ Syntax
*nowait* arg = *on* or *off*
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run
*version* arg = *2* or *3*
2 = use IMD version 2 (default)
3 = use IMD version 3. The subsequent keywords are only supported for version 3.
*time* arg = *on* or *off*
off = simulation time is not transmitted (default)
on = simulation time is transmitted.
*box* arg = *on* or *off*
off = simulation box data is not transmitted (default)
on = simulation box data is transmitted.
*coordinates* arg = *on* or *off*
off = atomic coordinates are not transmitted (default)
on = atomic coordinates are transmitted.
*velocities* arg = *on* or *off*
off = atomic velocities are not transmitted (default)
on = atomic velocities are transmitted.
*forces* arg = *on* or *off*
off = atomic forces are not transmitted (default)
on = atomic forces are transmitted.
Examples
""""""""
@ -41,10 +59,13 @@ Description
This fix implements the "Interactive MD" (IMD) protocol which allows
realtime visualization and manipulation of MD simulations through the
IMD protocol, as initially implemented in VMD and NAMD. Specifically
it allows LAMMPS to connect an IMD client, for example the `VMD visualization program <VMD_>`_, so that it can monitor the progress of the
it allows LAMMPS to connect an IMD client, for example the `VMD visualization program <VMD_>`_
(currently only supports IMDv2) or the
`Python IMDClient <IMDClient_>`_ (supports both IMDv2 and IMDv3),
so that it can monitor the progress of the
simulation and interactively apply forces to selected atoms.
If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD
If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD (-DCMAKE_CXX_FLAGS="-DLAMMPS_ASYNC_IMD" in CMake),
then fix imd will use POSIX threads to spawn a IMD communication
thread on MPI rank 0 in order to offload data reading and writing
from the main execution thread and potentially lower the inferred
@ -94,6 +115,13 @@ with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
In `IMDv3 <IMDv3_>`_, the protocol has been extended to allow for the transmission
of simulation time, box dimensions, atomic coordinates, velocities, and
forces. The *version* keyword allows to select the version of the
protocol to be used. The *time*, *box*, *coordinates*, *velocities*,
and *forces* keywords allow to select which data is transmitted to the
IMD client. The default is to transmit all data.
To connect VMD to a listening LAMMPS simulation on the same machine
with fix imd enabled, one needs to start VMD and load a coordinate or
topology file that matches the fix group. When the VMD command
@ -129,6 +157,10 @@ screen output is active.
.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
.. _IMDClient: https://github.com/Becksteinlab/imdclient/tree/main/imdclient
.. _IMDv3: https://imdclient.readthedocs.io/en/latest/protocol_v3.html
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""