IPKM/mdevaluate
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Added possibility to use more images with pbc_points.

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This commit is contained in:
sebastiankloth 2023-06-21 13:03:05 +02:00
parent a4b1105c54
commit a2164507d5
2 changed files with 24 additions and 14 deletions
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36
mdevaluate/pbc.py
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@ -198,28 +198,38 @@ def nojump(frame, usecache=True):
[m[:frame.step + 1, selection].sum(axis=0) for m in reader.nojump_matrixes] [m[:frame.step + 1, selection].sum(axis=0) for m in reader.nojump_matrixes]
).T) * frame.box.diagonal() ).T) * frame.box.diagonal()
return frame - delta return frame - delta
def pbc_points(coordinates, box, thickness=0, index=False, shear=False):
def pbc_points(coordinates, box, thickness=0, index=False, shear=False,
extra_image=False):
""" """
Returns the points their first periodic images. Does not fold Returns the points their first periodic images. Does not fold
them back into the box. them back into the box.
Thickness 0 means all 27 boxes. Positive means the box+thickness. Thickness 0 means all 27 boxes. Positive means the box+thickness.
Negative values mean that less than the box is returned. Negative values mean that less than the box is returned.
index=True also returns the indices with indices of images being their originals values. index=True also returns the indices with indices of images being their
originals values.
""" """
if shear: if shear:
box[2,0] = box[2,0]%box[0,0] box[2, 0] = box[2, 0] % box[0, 0]
grid = np.array([ [i, j, k] for k in [-1,0,1] for j in [1,0,-1] for i in [-1,0,1] ]) if shear or extra_image:
coordinatesPBC = np.concatenate([coordinates+v@box for v in grid], axis=0) grid = np.array([[i, j, k] for k in [-2, -1, 0, 1, 2]
for j in [2, 1, 0, -1, -2] for i in [-2, -1, 0, 1, 2]])
indices = np.tile(np.arange(len(coordinates)), 125)
else:
grid = np.array([[i, j, k] for k in [-1, 0, 1] for j in [1, 0, -1]
for i in [-1, 0, 1]])
indices = np.tile(np.arange(len(coordinates)), 27)
coordinates_pbc = np.concatenate([coordinates+v@box for v in grid], axis=0)
size = np.diag(box) size = np.diag(box)
indices = np.tile(np.arange(len(coordinates)),(27))
if thickness != 0: if thickness != 0:
mask = np.all(coordinatesPBC > -thickness, axis=1) mask = np.all(coordinates_pbc > -thickness, axis=1)
coordinatesPBC = coordinatesPBC[mask] coordinates_pbc = coordinates_pbc[mask]
indices = indices[mask] indices = indices[mask]
mask = np.all(coordinatesPBC < size+thickness, axis=1) mask = np.all(coordinates_pbc < size+thickness, axis=1)
coordinatesPBC = coordinatesPBC[mask] coordinates_pbc = coordinates_pbc[mask]
indices = indices[mask] indices = indices[mask]
if index: if index:
return coordinatesPBC, indices return coordinates_pbc, indices
return coordinatesPBC return coordinates_pbc

2
requirements.txt
View File

@ -6,5 +6,5 @@ pandas
dask dask
sqlalchemy sqlalchemy
psycopg2-binary psycopg2-binary
ipyvlume ipyvolume
jupyter_contrib_nbextensions jupyter_contrib_nbextensions