IPKM/mdevaluate
6
1
Fork 0
Code Issues 1 Pull Requests 1 Activity

apply selection and scaling with current box after delta in jumps has been cached or calculated directly. this should fix using nojump on NPT simulations #6

Open
robin wants to merge 2 commits from fix/nojump_and_npt_caching into main
pull from: fix/nojump_and_npt_caching
merge into: IPKM:main
Conversation 0 Commits 2 Files Changed 1 +9 -20
1 changed files with 9 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
src/mdevaluate/pbc.py
View File

@@ -149,32 +149,21 @@ def nojump(frame: CoordinateFrame, usecache: bool = True) -> CoordinateFrame:
i0 = 0
delta = 0
delta = (
delta
+ np.array(
np.vstack(
[m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
).T
)
@ frame.box
)
delta = (delta
+ np.vstack(
[m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
).T)
reader._nojump_cache[abstep] = delta
while len(reader._nojump_cache) > NOJUMP_CACHESIZE:
reader._nojump_cache.popitem(last=False)
delta = delta[selection, :]
else:
delta = (
np.array(
np.vstack(
[
m[: frame.step + 1, selection].sum(axis=0)
for m in reader.nojump_matrices
]
delta = np.vstack(
[m[: frame.step + 1, selection].sum(axis=0) for m in reader.nojump_matrices]
).T
)
@ frame.box
)
delta = delta[selection, :]
delta = np.array(delta @ frame.box)
return frame - delta