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[WIP] Start of fix for analysis with multiple expanded ensemble files. #35

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[WIP] Start of fix for analysis with multiple expanded ensemble files. #35

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24 changes: 17 additions & 7 deletions alchemical_analysis/parser_gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,36 +260,46 @@ def parseLog(self):
raise SystemExit("\nERROR!\nThere are more than 3 groups of files (%s, to be exact) each having different number of the dE columns; I cannot combine the data." % len(ndE_unique))

lv = numpy.array(lv, float) # *** Lambda vectors.
K = len(lv) # *** Number of lambda states.
K = len(lv) # *** Number of lambda states. # note, for expanded ensemble, this can change.

#===================================================================================================
# Preliminaries III: Count up the equilibrated snapshots.
#===================================================================================================

equiltime = P.equiltime
nsnapshots = numpy.zeros(K, int)

nsnapshots = None
for nf, f in enumerate(fs):

f.len_first, f.len_last = (len(line.split()) for line in unixlike.tailPy(f.filename, 2))
bLenConsistency = (f.len_first != f.len_last)

if f.bExpanded:


# number of files is not necessarily equal to the number of states.
equiltime = f.parseLog()
equilsnapshots = int(round(equiltime/f.snap_size))
f.skip_lines += equilsnapshots

extract_states = numpy.genfromtxt(f.filename, dtype=int, skiprows=f.skip_lines, skip_footer=1*bLenConsistency, usecols=1)
nsnapshots += numpy.array(Counter(extract_states).values())
current_nsnapshots = len(Counter(extract_states))
if nsnapshots == None:
nsnapshots = numpy.zeros(current_nsnapshots, int)
K = current_nsnapshots
else:
if len(nsnapshots) != current_nsnapshots:
print "Warning: number of states observed in %s (%d) does not match the number of states found in previous files (%d)" % (f.filename,current_nsnapshots,nsnapshots)
else:
nsnapshots += numpy.array(Counter(extract_states).values())

else:
nsnapshots = numpy.zeros(K, int)
equilsnapshots = int(equiltime/f.snap_size)
f.skip_lines += equilsnapshots
nsnapshots[nf] += unixlike.wcPy(f.filename) - f.skip_lines - 1*bLenConsistency

print "First %s ps (%s snapshots) will be discarded due to equilibration from file %s..." % (equiltime, equilsnapshots, f.filename)

#===================================================================================================
# Preliminaries IV: Load in equilibrated data.
#===================================================================================================
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