Particle Density

Description

Compute the average particle mass density using uniform binning. The mass value used is the atomic weight for each particle.

Input Ports

structure_in MoleculeType Molecular structure data.

Parameters

Select atoms atoms selection widget The list of atoms contained in the input structure. The list could show individual atoms or element types. A buttom permits clearing the selection. The freeze toggle disable the selection and make possible saving the selection in the application.
Selection mode radio buttons Select the kind of operation:
Pass selected
Pass to output only the atoms selected in the list
Remove selected
Remove from the structure only the atoms selected in the list
Use mass toggle If set, use atoms masses in computing density, otherwise use only the number of atoms.
Use cubic cells toggle If set the number of cells on each side is changed to obtain roughly cubic cells.
Cells per side numeric field The number of cells on each side of the volume.
Smoothing numeric field The smoothing factor for the gaussian. If set the particle mass is splattered on a Kernel size grid with sigma equal to this value.
Kernel size radio buttons The number of cells on each side of the gaussian smoothing kernel. This control is enabled only if Smoothing is greather than zero.
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.

Output Ports

selected_atoms MoleculeType The atoms selected by the module.
fld_density Field_Unif The resulting volume with average mass density associated to each volume cell.
obj_density DefaultObject The renderable version of fld_density.
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