Tracker Form

Figure 4.16: The Tracker form

The Tracker form is used to set up external 3D pointers, buttons, force-feedback devices, and the VMD ``tools'' that they control.

Supported devices and how to configure them

VMD currently can only communicate with devices in two ways: through the CAVE software or using the Virtual Reality Peripheral Network (VRPN). VRPN is a system which allows workstations to use many types of devices over the network. This means that VMD does not have to be running on the same computer that the devices are plugged into. In the CAVE, VMD recognizes two types of devices: buttons and three-dimensional trackers. With VRPN, you may use buttons, trackers, and also force-feedback (haptic) devices such as the PHANToM. More types of devices may be added in the future.

To use these kinds of devices with VMD, you need to create a sensor configuration file, in your home directory, called .vmdsensors. In this file, any number of devices can be specified, using a universal sensor locator (USL). The format for a USL is as follows:

• USL - type://place/name:nums
• type - the type of sensor (vrpntracker, vrpnbuttons, vrpnfeedback, cavetracker, or cavebuttons)
• place - the machine that controls it. Devices that cannot yet be used on arbitrary computers over the network must have the keyword local here to be compatible with future versions.
• name - the name of the device within that machine. If multiple devices can't currently exist, such as with the CAVE, then a standard name should be used, such as cave, so that the same USL will make sense in the future, when multiple devices are allowed.
• nums - a comma-separated list of numbers of devices belonging to that names (optional, defaults to zero). Some devices demand only one number or a specific number but button devices should work correctly now.

The lines of a sensor configuration file come in four flavors:

• Comments begin with # and are ignored.
• Empty lines are also ignored.
• Device lines have the form device name USL, where name is the name that VMD will use to refer to the device, and USL is the device's USL.
• Options tell VMD how to use the most recently listed device. Currently, there are four supported options:
  • ``scale $x$'' scales the position of a tracker by a factor $x$.
  • ``offset $x$ $y$ $z$'' adds a constant vector to the position of a tracker.
  • ``rot right|left $A_{00}$ $A_{01}\ldots A_{33}$'' multiplies the orientation matrix returned by a tracker on either the right or the left by the matrix $A$.
  • ``forcescale $x$'' multiplies the force applied to a force-feedback device by the amount $x$.

Here is an example, showing all the possible things you can do with a sensor configuration file:

# the PHANToM connected to the computer "odessa"
device phantomtracker vrpntracker://odessa/Phantom0
scale 10
rot left 0 0 -1 0 1 0 1 0 0

device phantombuttons vrpnbuttons://odessa/Phantom0
device   phantomfeedback vrpnfeedback://odessa/Phantom0

# Polhemus fastrak on titan
device fastrak1 vrpntracker://titan/Tracker0:0
rot right 0 0 1 1 0 0 0 1 0
rot left 0 0 -1 -1 0 0 0 -1 0
device fastrak2 vrpntracker://titan/Tracker0:1
rot right 0 0 1 1 0 0 0 1 0
rot left 0 0 -1 -1 0 0 0 -1 0

#### Configuration for the CAVE
# CAVE tracker
device cavetracker cavetracker://cave/cave
scale 0.32
offset 0 -3.03 0

# CAVE buttons
device cavebuttons cavebuttons://cave/cave:0,1,2,3

# CAVE buttons (for left-handers)
device cavebuttons cavebuttons://cave/cave:3,2,1,0

Using devices with VMD

There are several different ``tools'', each of which can be used with any of the input devices^4.1:

• The Grab Tool mimics a pair of tweezers, and can be used to move molecules around on the screen without any keyboard or mouse commands. Pressing a button connects the 3d cursor to the nearest molecule. Then, moving or rotating the tracker will cause the molecule to move or rotate around on the screen.

• The Rotate Tool is a tool for precisely rotating molecules with haptic devices. When a button is pressed and released, the cursor is again connected to the molecule. With this tool, however, the center of the molecule is fixed, and the end of the haptic pointer is forced to lie on the surface of a sphere about this center. Moving the device around the surface of the sphere rotates the molecule, and another button click releases the molecule. There are detentes -- like the clicks commonly felt in a 2d dial -- on the surface of the sphere, arranged so that the user can rotate the molecule to precise 90-degree points. If the user holds down the button for a while initially, he can feel the sphere and the detentes, but do not affect the molecule. This ``preview mode'' allows the user to find a good point from which to start the rotation.

• The Joystick Tool is the three-dimensional equivalent of a Joystick, for haptic devices. Pressing the button creates a virtual ``spring,'' holding the device to its current location. If it is pushed away from this point in some direction, the selected molecule starts sliding in that direction, with a velocity that is proportional to the displacement of the device. The joystick tool shows how a three dimensional input device can be used to supply relative (differential) coordinates instead of absolute coordinates.

• The Tug Tool is a tool that allows interaction with running molecular dynamics simulations. Pressing the button connects the device with a simulated spring to the nearest atom, and pulling on it adds a force to the simulation. If a haptic device is being used, the user will feel a force on his hand that is proportional to this force. In this way, the tug tool implements something like the click-and-drag that is commonly used with windowing systems.

  If an atom selection is assigned to the Tools, as described in section 4.4.6, the the Tug Tool will apply a force to all the atoms in the selection. The force applied will be proportional to the masses of the atoms in the selection, so that all atoms experience the same acceleration. When a Tool Selection has been assigned, the Tug Tool will always affect that selection, even if the button is pressed far from any atoms in the selection; this is intended to make it easier for the user to apply forces only on those atoms he/she intends to steer.

• The Pinch Tool is similar to the Tug Tool, except that force is applied only along the axis defined by the orientation of the tracker.

• The SMD Tool is a tool intended for use with steered molecular dynamics (SMD). It allows the user to pull on atoms in only one direction, so that the forces and motions of the molecule can be more easily analyzed. The user clicks at a ``target point'', drags the pointer back to the atom he wishes to pull on, then releases the button. The tool now behaves like a tug tool, but forces are restricted to lie parallel to the line through the atom and the target point. Using the SMD tool with a haptic device feels like pushing against a non-rotating, frictionless plane, since the forces applied to the user's hand must also all point parallel to this line. The force applied and the position of the atom are automatically recorded to the file pull.txt.

To add a new tool to a VMD session, open the tracker form and click the Create Tool button. The tool's number and type are displayed in the list to the left. Devices can be added to the tool by selecting them from the Add Device menu, or removed with the Delete Device button. Some of the options that can be specified in the sensor configuration file can be edited in using the controls below, and the tool's type can be changed with the Type menu.