Accumulate Traces

Description

Accumulate traces (accumulated positions) for specific atoms in a sequence of time steps. The accumulator is an uniformly subdivided volume. For each time step the count associated to cells containig selected atoms are incremented. Also the positions of the atoms are saved to create the lines of evolution of each atom.

If the input molecule contains unit cell data the traces are split so if one of them exit from a side of the unit cell and reenters from the opposite side, no cross unit cell segments appears.

Input Ports

structure_in MoleculeType Molecular structure data. The structure should be part of a trajectory.

Parameters

Select atoms to trace atom select list The list of atoms contained in the molecule.
Marker side numeric field Side of the marker for the selected atoms. The marker disappears selecting the "freeze selection" toggle.
Active toggle Enable the module. For each step update the accumulator.
Clear button Empties the accumulator.
Accumulator side numeric field The number of cells on each side of the accumulator.
use manual limits toggle For the accumulator volume use the limits entered below. If not set the volume limits are computed by the module and show in the fields below.
X, Y, Z min numeric fields Lower coordinates values for the volume.
X, Y, Z max numeric fields Upper coordinates values for the volume.
Select rendering method radio buttons The object output could be volume render or line. It can be:
Volume render
the obj_trace output is connected to a volume rendering module (Occupancy volume render) that show the occupancy volume.
Line traces
each traced atom leaves a line trace.
Not visible
no output is generated.
Trace split tolerance numeric field To split a trace that jumps from one side to another of the unit cell the criteria is the relative difference between the trace segment length and unit cell lenght (side or diagonal). Increase this value if the traces have long streak between unit cell facies.

Output Ports

marker DefaultObject Themarker on the selected atoms to trace.
obj_trace DefaultObject The renderable version of out_trace (volume render or line rendering).
out_occupancy Field_Unif The accumulator. Each node contains a count of the accumulated presences of the traced atoms in the corresponding accumulator cell.
out_trace Mesh+Node_Data For each traced atom this field contains a polyline passing through all its visited positions. The associated value is the timestep.

See also

Example

stm4-examples/Accumulate_TracesEx.v — Remember to select H atoms before beginning.

Return to index