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Changed pbc_points to allow to shift the box in the other direction for shear simulations.

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sebastiankloth
2023-06-28 13:53:37 +02:00
parent 8146a9b270
commit 76e44dde49
1 changed files with 9 additions and 19 deletions
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28
mdevaluate/pbc.py
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@@ -241,9 +241,7 @@ def nojump(frame, usecache=True):
return frame - delta return frame - delta
def pbc_points( def pbc_points(coordinates, box, thickness=0, index=False, shear=False):
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.
@@ -253,22 +251,14 @@ def pbc_points(
originals values. originals values.
""" """
if shear: if shear:
box[2, 0] = box[2, 0] % box[0, 0] box[2, 0] = box[2, 0] % box[2, 2]
if shear or extra_image: if box[2, 0] > box[2, 2]:
grid = np.array( box[2, 0] = box[2, 0] - box[2, 2]
[
[i, j, k] grid = np.array(
for k in [-2, -1, 0, 1, 2] [[i, j, k] for k in [-1, 0, 1] for j in [1, 0, -1] for i in [-1, 0, 1]]
for j in [2, 1, 0, -1, -2] )
for i in [-2, -1, 0, 1, 2] indices = np.tile(np.arange(len(coordinates)), 27)
]
)
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) coordinates_pbc = np.concatenate([coordinates + v @ box for v in grid], axis=0)
size = np.diag(box) size = np.diag(box)