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Add back decorrelation #31

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merged 1 commit into from
Jun 14, 2023
Merged

Add back decorrelation #31

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12 changes: 5 additions & 7 deletions safep/processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,19 +133,17 @@ def read_and_process(fepoutFiles, temperature, decorrelate, detectEQ):
"""
Read NAMD fepout files for a single calculation and carry out any decorrelation or equilibrium detection
Arguments: files to parse, temperature, decorrelate (boolean, whether or not to use alchemlyb's decorrelation functions), detectEQ (boolean, whether or not to use alchemlyb's equilibrium detection)
Returns: u_nk, affix (a string that describes the data processing)
Returns: u_nk
"""
fepoutFiles = natsorted(fepoutFiles)
u_nk = namd.extract_u_nk(fepoutFiles, temperature)

affix = ""

if detectEQ:
print("Detecting Equilibrium")
affix = f"{affix}_AutoEquilibrium"
print("Detecting Equilibrium (includes decorrelating)")
u_nk = detect_equilibrium_u_nk(u_nk)
else:
affix = f"{affix}_HardEquilibrium"
elif decorrelate:
print(f"Decorrelating samples")
u_nk = decorrelate_u_nk(u_nk)

return u_nk

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