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Slicing in a loop

Anders Bråte
Anders Bråte
1 Post
#1 · November 30, 2021, 6:45 pm

Hi, I'm attempting to slice away pieces of a system to study the slice further, however my script does not behave as expected. I've seen some previous post regarding slicing in a loop over timesteps, however this is simply a loop over the grid to slice away each portion of it. Does ovito not like slicing in loops?

This code slices away squares of a NxN grid. When i print out (i+1)*lx etc and retrace the steps in graphical ovito i'm left with a nice slice of the system, however the ovito.io export_file call says there is no data to be exported.

for i in range(grid[0]): #grid is a tuple of system dimension ex (3,3)
    for j in range(grid[1]):
        if bool_grid[i,j]: #is boo_grid is 1, we have an asperity
            print('asperity at', i,j)
            #lx ly is size of one square

            # first outward slice X direction
            pipeline.modifiers.append(SliceModifier(
                                      distance = (i+1)*lx,
                                      normal = (1.0, 0.0, 0.0)))

            # first inward slice X direction
            pipeline.modifiers.append(SliceModifier(
                                      distance = (i)*lx,
                                      normal = (1.0, 0.0, 0.0),
                                      inverse = True))

            # first outward slice Y direction
            pipeline.modifiers.append(SliceModifier(
                                      distance = (j+1)*ly,
                                      normal = (0.0, 1.0, 0.0)))

            # first outward slice Y direction
            pipeline.modifiers.append(SliceModifier(
                                      distance = (j)*ly,
                                      normal = (0.0, 1.0, 0.0),
                                      inverse = True))


            export_file(pipeline, 'test_block_asperity{}'.format(asperity), 'lammps/data', atom_style = 'atomic')

            del pipeline.modifiers

For context i'll add a couple of screenshots of the system and what i'm trying to achieve.

Thanks in advance for any help

Uploaded files:
  • temp_erratic_system.png
  • temp_erratic_slice.png
Constanze Kalcher
Constanze Kalcher
562 Posts
#2 · December 1, 2021, 10:52 am

Hi Anders,

I can't tell you exactly what is going wrong since I don't have the complete code, but I think this can be simplified by using an ExpressionSelectionModifier. This should work as expected:

for i in range(grid[0]): #grid is a tuple of system dimension ex (3,3)
    for j in range(grid[1]):
        if bool_grid[i,j]: #is boo_grid is 1, we have an asperity
            print('asperity at', i,j)
            data = pipeline.compute() 
            expression = f"Position.X >= {i*lx} && Position.X < {(i+1)*lx} && Position.Y >= {j*ly} && Position.Y < {(j+1)*ly}"
            data.apply(ExpressionSelectionModifier(expression = expression))
            data.apply(InvertSelectionModifier())
            data.apply(DeleteSelectedModifier())
            export_file(data, f'test_block{i}{j}.data', 'lammps/data', atom_style = 'atomic')

 

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