Upon initialization of the fix, it will open a communication port -on the node with MPI task 0 and wait for an incoming connection. -As soon as an IMD client is connected, the simulation will continue -and the fix will send the current coordinates of the fix's group -to the IMD client at every trate MD step. When using r-RESPA, trate -applies to the steps of the outmost RESPA level. -During a run with an active IMD connection also the IMD client can -request to apply forces to selected atoms of the fix group. +
Upon initialization of the fix, it will open a communication port on +the node with MPI task 0 and wait for an incoming connection. As soon +as an IMD client is connected, the simulation will continue and the +fix will send the current coordinates of the fix's group to the IMD +client at every trate MD step. When using r-RESPA, trate applies to +the steps of the outmost RESPA level. During a run with an active IMD +connection also the IMD client can request to apply forces to selected +atoms of the fix group.
-The port number selected must be an available network port number. -On many machines, port numbers < 1024 are reserved for accounts with -system manager privilege and specific applications. If multiple imd -fixes would be active at the same time, each needs to use a different +
The port number selected must be an available network port number. On +many machines, port numbers < 1024 are reserved for accounts with +system manager privilege and specific applications. If multiple imd +fixes would be active at the same time, each needs to use a different port number.
-The trate keyword allows to select how often the coordinate data -is sent to the IMD client. It can also be changed on request of -the IMD client through an IMD protocol message. -The unwrap keyword allows to send "unwrapped" coordinates to -the IMD client that undo the wrapping back of coordinates into -the principle unit cell, as done by default in LAMMPS. -The fscale keyword allows to apply a scaling factor to forces -transmitted by the IMD client. The IMD protocols stipulates that -forces are transferred in kcal/mol/angstrom under the assumption -that coordinates are given in angstrom. For LAMMPS runs 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. +
The nowait keyword controls the behavior of the fix when no IMD +client is connected. With the default setting of off, LAMMPS will +wait until a connection is made before continuing with the +execution. Setting nowait to on will have the LAMMPS code be ready +to connect to a client, but continue with the simulation. This can for +example be used to monitor the progress of an ongoing calculation +without the need to be permanently connected or having to download a +trajectory file.
-To connect VMD to a waiting 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 prompts appears, one types the command line: +
The trate keyword allows to select how often the coordinate data is +sent to the IMD client. It can also be changed on request of the IMD +client through an IMD protocol message. The unwrap keyword allows +to send "unwrapped" coordinates to the IMD client that undo the +wrapping back of coordinates into the principle unit cell, as done by +default in LAMMPS. The fscale keyword allows to apply a scaling +factor to forces transmitted by the IMD client. The IMD protocols +stipulates that forces are transferred in kcal/mol/angstrom under the +assumption that coordinates are given in angstrom. For LAMMPS runs +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. +
+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 +prompts appears, one types the command line:
imd connect localhost 5678
This assumes that fix imd was started with 5678 as a port number for the IMD protocol.
-The steps to do interactive manipulation of a running simulation -in VMD are the following: +
The steps to do interactive manipulation of a running simulation in +VMD are the following:
-In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom". -You may alternately select "Residue", or "Fragment" to apply forces to -whole residues or fragments. Your mouse can now be used to apply forces -to your simulation. Click on an atom, residue, or fragment and drag to -apply a force. Click quickly without moving the mouse to turn the force -off. You can also use a variety of 3D position trackers to apply forces -to your simulation. Trackers with force-feedback such as the Sensable -PHANTOM allow you to feel the forces you are applying to your molecules, -as if they were real objects. See the VMD IMD Homepage for -more details. +
In the Mouse menu of the VMD Main window, select "Mouse -> Force -> +Atom". You may alternately select "Residue", or "Fragment" to apply +forces to whole residues or fragments. Your mouse can now be used to +apply forces to your simulation. Click on an atom, residue, or +fragment and drag to apply a force. Click quickly without moving the +mouse to turn the force off. You can also use a variety of 3D position +trackers to apply forces to your simulation. Trackers with +force-feedback such as the Sensable PHANTOM allow you to feel the +forces you are applying to your molecules, as if they were real +objects. See the VMD IMD Homepage for more details.
If IMD control messages are received, a line of text describing the message and its effect will be printed to the LAMMPS output screen, if @@ -133,8 +144,8 @@ group the fix is applied to. The fix internally sorts atom IDs by ascending integer value; in VMD (and thus the IMD protocol) those will be assigned 0-based consecutive index numbers.
-When using multiple active IMD connections at the same time, -each needs to use a different port number. +
When using multiple active IMD connections at the same time, each +needs to use a different port number.
Related commands: none
diff --git a/doc/fix_imd.txt b/doc/fix_imd.txt index 0e2fb29a36..b1125cbd19 100644 --- a/doc/fix_imd.txt +++ b/doc/fix_imd.txt @@ -21,7 +21,10 @@ keyword = {unwrap} or {fscale} or {trate} :l on = "unwrapped" coordinates using the image flags used {fscale} arg = factor factor = floating point number to scale IMD forces (default: 1.0) - {trate} arg = transmission rate of coordinate data sets (default: 1) :pre + {trate} arg = transmission rate of coordinate data sets (default: 1) + {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 :pre :ule [Examples:] @@ -42,58 +45,66 @@ Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. We thank them for providing a software interface that allows codes like LAMMPS to hook to "VMD"_VMD. -Upon initialization of the fix, it will open a communication port -on the node with MPI task 0 and wait for an incoming connection. -As soon as an IMD client is connected, the simulation will continue -and the fix will send the current coordinates of the fix's group -to the IMD client at every trate MD step. When using r-RESPA, trate -applies to the steps of the outmost RESPA level. -During a run with an active IMD connection also the IMD client can -request to apply forces to selected atoms of the fix group. +Upon initialization of the fix, it will open a communication port on +the node with MPI task 0 and wait for an incoming connection. As soon +as an IMD client is connected, the simulation will continue and the +fix will send the current coordinates of the fix's group to the IMD +client at every trate MD step. When using r-RESPA, trate applies to +the steps of the outmost RESPA level. During a run with an active IMD +connection also the IMD client can request to apply forces to selected +atoms of the fix group. -The port number selected must be an available network port number. -On many machines, port numbers < 1024 are reserved for accounts with -system manager privilege and specific applications. If multiple imd -fixes would be active at the same time, each needs to use a different +The port number selected must be an available network port number. On +many machines, port numbers < 1024 are reserved for accounts with +system manager privilege and specific applications. If multiple imd +fixes would be active at the same time, each needs to use a different port number. -The {trate} keyword allows to select how often the coordinate data -is sent to the IMD client. It can also be changed on request of -the IMD client through an IMD protocol message. -The {unwrap} keyword allows to send "unwrapped" coordinates to -the IMD client that undo the wrapping back of coordinates into -the principle unit cell, as done by default in LAMMPS. -The {fscale} keyword allows to apply a scaling factor to forces -transmitted by the IMD client. The IMD protocols stipulates that -forces are transferred in kcal/mol/angstrom under the assumption -that coordinates are given in angstrom. For LAMMPS runs 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. +The {nowait} keyword controls the behavior of the fix when no IMD +client is connected. With the default setting of {off}, LAMMPS will +wait until a connection is made before continuing with the +execution. Setting {nowait} to {on} will have the LAMMPS code be ready +to connect to a client, but continue with the simulation. This can for +example be used to monitor the progress of an ongoing calculation +without the need to be permanently connected or having to download a +trajectory file. -To connect VMD to a waiting 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 prompts appears, one types the command line: +The {trate} keyword allows to select how often the coordinate data is +sent to the IMD client. It can also be changed on request of the IMD +client through an IMD protocol message. The {unwrap} keyword allows +to send "unwrapped" coordinates to the IMD client that undo the +wrapping back of coordinates into the principle unit cell, as done by +default in LAMMPS. The {fscale} keyword allows to apply a scaling +factor to forces transmitted by the IMD client. The IMD protocols +stipulates that forces are transferred in kcal/mol/angstrom under the +assumption that coordinates are given in angstrom. For LAMMPS runs +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. + +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 +prompts appears, one types the command line: imd connect localhost 5678 :pre This assumes that {fix imd} was started with 5678 as a port number for the IMD protocol. -The steps to do interactive manipulation of a running simulation -in VMD are the following: +The steps to do interactive manipulation of a running simulation in +VMD are the following: -In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom". -You may alternately select "Residue", or "Fragment" to apply forces to -whole residues or fragments. Your mouse can now be used to apply forces -to your simulation. Click on an atom, residue, or fragment and drag to -apply a force. Click quickly without moving the mouse to turn the force -off. You can also use a variety of 3D position trackers to apply forces -to your simulation. Trackers with force-feedback such as the Sensable -PHANTOM allow you to feel the forces you are applying to your molecules, -as if they were real objects. See the "VMD IMD Homepage"_imdvmd for -more details. +In the Mouse menu of the VMD Main window, select "Mouse -> Force -> +Atom". You may alternately select "Residue", or "Fragment" to apply +forces to whole residues or fragments. Your mouse can now be used to +apply forces to your simulation. Click on an atom, residue, or +fragment and drag to apply a force. Click quickly without moving the +mouse to turn the force off. You can also use a variety of 3D position +trackers to apply forces to your simulation. Trackers with +force-feedback such as the Sensable PHANTOM allow you to feel the +forces you are applying to your molecules, as if they were real +objects. See the "VMD IMD Homepage"_imdvmd for more details. If IMD control messages are received, a line of text describing the message and its effect will be printed to the LAMMPS output screen, if @@ -124,8 +135,8 @@ group the fix is applied to. The fix internally sorts atom IDs by ascending integer value; in VMD (and thus the IMD protocol) those will be assigned 0-based consecutive index numbers. -When using multiple active IMD connections at the same time, -each needs to use a different port number. +When using multiple active IMD connections at the same time, each +needs to use a different port number. [Related commands:] none