update FAQ / basic philosophy #341

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1. orbeckst commented on Nov 9, 2023

   

   orbeckst

   on Nov 9, 2023

   Last edited by orbeckst

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   From discord #users:

   Q:How to make spatial selections relative to a FIXED point?

   I'm trying to create a group using select_atoms and the cylayer keyword. However, reading the doc I've noticed that the selection argument has to be a group. Is there a way to use the cylayer keyword centered around a specific xyz coordinate in my box?

   A: Explicit selection with PBC

   For high performance you might actually not use selections but do explicit calculations with the positions. Importantly, we have to take periodic boundaries into account with using MDAnalysis.lib.distances.minimize_vectors():

   import numpy as np
   import MDAnalysis as mda
   from MDAnalysis.lib import distances
   from MDAnalysisTests import datafiles as data
   
   # make a universe to work with, this should really be YOUR data
   u = mda.Universe(data.TPR, data.XTC)
   
   # cyzone geometric parameters
   # center should be located INSIDE the simulation box
   center = np.array([-10.2, 0, 3.6])
   zmax, zmin = 25, 5
   rInner, rOuter = 5, 10 
   
   ag = u.select_atoms("resname SOL and name OW") # just oxygen for simplicity
   
   # calculate distance from center WITH PBC
   x = distances.minimize_vectors(ag.positions - center, ag.dimensions)
   
   # make geometric selections
   within_z_limits = (zmin < x[:, 2]) & (x[:, 2] < zmax)
   radii = np.linalg.norm(x[:, :2], axis=1)
   within_r = (rInner < radii) & (radii < rOuter)
   within_cyzone = within_r & within_z_limits
   
   # get atoms that fulfill geometric criteria
   layer = ag[within_cyzone]

   NOT WORKING: Use a fake AtomGroup with a fixed dummy atom

   EDIT: Unfortunately, this does not work as expected because the selections are still made inside the same universe.* I tried out different positions and didn't manage to shift the selection.

   Yes, you're right, the selection argument in cylayer innerRadius externalRadius zMax zMin selection has to be something that selects atoms. But it is more general: it can be any AtomGroup so we can use the group keyword to insert an arbitrary AtomGroup as the reference point via

   u.select_atoms("cylayer {innerRadius} {externalRadius} {zMax} {zMin} group myGroup", myGroup=some_atomgroup)

   We can craft an AtomGroup that contains a fake atom with a fixed coordinate (using the very flexible Universe.empty():

   import MDAnalysis as mda
   from MDAnalysisTests import datafiles as data
   
   # make a universe to work with, this should really be YOUR data
   u = mda.Universe(data.TPR, data.XTC)
   
   # create a fake universe with a single atom as a fixed reference
   fixed = mda.Universe.empty(n_atoms=1, trajectory=True)
   # set the coordinates to what you need (this sets all atoms to the same value, but we only have one)
   fixed.atoms.positions = [-10.2, 0, 3.6]
   
   # select with the fixed reference group to anchor cyzone
   # (you probably want updating=True if the contents of the selection should change
   # along a trajectory)
   layer = u.select_atoms("resname SOL and cylayer 5 10 25 5 group REFERENCE", REFERENCE=fixed.atoms, updating=True)

   Now layer is your selected AtomGroup. Note that you could just provide reference.atoms as part of the selection and that these groups do not have to come from the same Universe! This gives you a lot of flexibility.

   Do double check (eg by writing out frames and visually checking) that this works as expected