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Fixed parse jumps for triclinic box case

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This commit is contained in:
Sebastian Kloth 2024-01-30 16:27:59 +01:00
parent 3e8fd04726
commit 77771738ab
1 changed files with 17 additions and 3 deletions
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20
src/mdevaluate/reader.py
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@ -187,19 +187,33 @@ def nojump_save_filename(reader: BaseReader):
def parse_jumps(trajectory: Coordinates):
prev = trajectory[0].whole
box = prev.box.diagonal()
box = prev.box
SparseData = namedtuple("SparseData", ["data", "row", "col"])
jump_data = (
SparseData(data=array("b"), row=array("l"), col=array("l")),
SparseData(data=array("b"), row=array("l"), col=array("l")),
SparseData(data=array("b"), row=array("l"), col=array("l")),
)
for i, curr in enumerate(trajectory):
if i % 500 == 0:
logger.debug("Parse jumps Step: %d", i)
delta = ((curr - prev) / box).round().astype(np.int8)
r3 = np.subtract(curr, prev)
delta_z = np.array(np.rint(np.divide(r3[:, 2], box[2][2])), dtype=np.int8)
r2 = np.subtract(
r3,
(np.rint(np.divide(r3[:, 2], box[2][2])))[:, np.newaxis]
* box[2][np.newaxis, :],
)
delta_y = np.array(np.rint(np.divide(r2[:, 1], box[1][1])), dtype=np.int8)
r1 = np.subtract(
r2,
(np.rint(np.divide(r2[:, 1], box[1][1])))[:, np.newaxis]
* box[1][np.newaxis, :],
)
delta_x = np.array(np.rint(np.divide(r1[:, 0], box[0][0])), dtype=np.int8)
delta = np.array([delta_x, delta_y, delta_z]).T
prev = curr
box = prev.box
for d in range(3):
(col,) = np.where(delta[:, d] != 0)
jump_data[d].col.extend(col)