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lammps
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some more whitespace cleanup

This commit is contained in:
Axel Kohlmeyer 2019-09-17 16:10:14 -04:00
parent fd63b08f99
commit 28b634f20d
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GPG Key ID: D9B44E93BF0C375A
2 changed files with 6 additions and 6 deletions
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6
tools/replica/example/parse_ene.py
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@ -15,16 +15,16 @@ for i in range(ntemps):
logfn = '%s.%d' % (logfnprefix, i) logfn = '%s.%d' % (logfnprefix, i)
with open(logfn, 'r') as of: with open(logfn, 'r') as of:
lines = of.readlines() lines = of.readlines()
# extract relevant lines from logfile # extract relevant lines from logfile
start = [lines.index(line) for line in lines if line.startswith(start_token)][0] start = [lines.index(line) for line in lines if line.startswith(start_token)][0]
lines = lines[(start+1) : ] lines = lines[(start+1) : ]
stop = [lines.index(line) for line in lines if line.startswith(end_token)][0] stop = [lines.index(line) for line in lines if line.startswith(end_token)][0]
lines = lines[:stop] lines = lines[:stop]
# store the potential energies # store the potential energies
pe = [float(line.strip().split()[-1]) for line in lines] pe = [float(line.strip().split()[-1]) for line in lines]
u_kn.append(pe) u_kn.append(pe)
u_kn = np.array(u_kn) u_kn = np.array(u_kn)
np.savetxt('ene.peptide', u_kn, fmt = '%5.5f') np.savetxt('ene.peptide', u_kn, fmt = '%5.5f')

6
tools/replica/reorder_remd_traj.py
View File

@ -351,7 +351,7 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
u_kln = np.zeros([ntemps, ntemps, nframes], float) u_kln = np.zeros([ntemps, ntemps, nframes], float)
for k in range(ntemps): for k in range(ntemps):
u_kln[k] = np.outer(beta_k, u_kn[k]) u_kln[k] = np.outer(beta_k, u_kn[k])
# run pymbar and extract the free energies # run pymbar and extract the free energies
print("\nRunning pymbar...") print("\nRunning pymbar...")
mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True) mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True)
@ -368,7 +368,7 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
denom = f_k - beta_k[k] * u_kn[k,n] denom = f_k - beta_k[k] * u_kn[k,n]
for l in range(ntemps): for l in range(ntemps):
logw[l][k,n] = num - logsumexp(denom) - log_nframes logw[l][k,n] = num - logsumexp(denom) - log_nframes
return logw return logw
@ -518,7 +518,7 @@ if __name__ == "__main__":
# open all replica files for reading # open all replica files for reading
infobjs = [readwrite(i, "rb") for i in intrajfns] infobjs = [readwrite(i, "rb") for i in intrajfns]
# open all byteindex files # open all byteindex files
byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) ) byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) )