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Merge branch 'reorder_remd_traj' of github.com:tanmoy7989/lammps into reorder_remd_traj

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# Conflicts:
#	tools/replica/reorder_remd_traj.py
This commit is contained in:
Axel Kohlmeyer
2019-09-17 16:09:13 -04:00
parent 636a8aaef9 cde16580c0
commit fd63b08f99
5 changed files with 51 additions and 42 deletions
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33
doc/src/Tools.txt
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@ -76,10 +76,10 @@ Post-processing tools :h3
"pymol_asphere"_#pymol,
"python"_#pythontools,
"reax"_#reax_tool,
"replica"_#replica,
"smd"_#smd,
"spin"_#spin,
"xmgrace"_#xmgrace,
"replica"_#replica :tb(c=6,ea=c,a=l)
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
Miscellaneous tools :h3
@ -486,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts.
:line
replica tool :h4,link(replica)
The tools/replica directory contains the reorder_remd_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided.
This tool was written by (and is maintained by) Tanmoy Sanyal,
while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
:line
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alone codes that can
@ -551,17 +566,3 @@ See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)
:line
replica tool :h4,link(replica)
The tools/replica directory contains the reorder_remd_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided.
This tool was written by Tanmoy Sanyal, while at the Shell lab
at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)

8
doc/src/temper.txt
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@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one
dump file with snapshots at 300K (from all replicas), another with
snapshots at 310K, etc. Note that these new dump files will not
contain "continuous trajectories" for individual atoms, because two
successive snapshots (in time) may be from different replicas.
successive snapshots (in time) may be from different replicas. The
reorder_remd_traj python script can do the reordering for you
(and additionally also calculated configurational log-weights of
trajectory snapshots in the canonical ensemble). The script can be found
in the tools/replica directory while instructions on how to use it is
available in doc/Tools (in brief) and as a README file in tools/replica
(in detail).
The last argument {index} in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one

1
tools/README
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@ -38,6 +38,7 @@ polybond Python tool for programmable polymer bonding
pymol_asphere convert LAMMPS output of ellipsoids to PyMol format
python Python scripts for post-processing LAMMPS output
reax Tools for analyzing output of ReaxFF simulations
replica tool to reorder LAMMPS replica trajectories according to temperature
smd convert Smooth Mach Dynamics triangles to VTK
spin perform a cubic polynomial interpolation of a GNEB MEP
vim add-ons to VIM editor for editing LAMMPS input scripts

2
tools/replica/example/in.peptide
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@ -14,7 +14,7 @@ dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data ../../../examples/peptide/data.peptide
read_data data.peptide
neighbor 2.0 bin
neigh_modify delay 5

49
tools/replica/reorder_remd_traj.py
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@ -38,11 +38,11 @@ StringIO (or io if in Python 3.x)
import os, sys, numpy as np, argparse, time, pickle
import os, numpy as np, argparse, time, pickle
from scipy.special import logsumexp
from mpi4py import MPI
from tqdm import tqdm, trange
from tqdm import tqdm
import gzip, bz2
try:
# python-2
@ -78,12 +78,10 @@ def _get_nearest_temp(temps, query_temp):
"""
if isinstance(temps, list): temps = np.array(temps)
idx = np.argmin(abs(temps - query_temp))
out_temp = temps[idx]
return out_temp
return temps[np.argmin(np.abs(temps-query_temp))]
def readwrite(trajfn, mode = "rb"):
def readwrite(trajfn, mode):
"""
Helper function for input/output LAMMPS traj files.
Trajectories may be plain text, .gz or .bz2 compressed.
@ -96,11 +94,14 @@ def readwrite(trajfn, mode = "rb"):
"""
if trajfn.endswith(".gz"):
return gzip.GzipFile(trajfn, mode)
of = gzip.open(trajfn, mode)
#return gzip.GzipFile(trajfn, mode)
elif trajfn.endswith(".bz2"):
return bz2.BZ2File(trajfn, mode)
of = bz2.open(trajfn, mode)
#return bz2.BZ2File(trajfn, mode)
else:
return file(trajfn, mode)
of = open(trajfn, mode)
return of
def get_replica_frames(logfn, temps, nswap, writefreq):
@ -163,7 +164,7 @@ def get_byte_index(rep_inds, byteindfns, intrajfns):
if os.path.isfile(byteindfns[n]): continue
# extract bytes
fobj = readwrite(intrajfns[n])
fobj = readwrite(intrajfns[n], "rb")
byteinds = [ [0,0] ]
# place file pointer at first line
@ -243,7 +244,7 @@ def write_reordered_traj(temp_inds, byte_inds, outtemps, temps,
for n in temp_inds:
# open string-buffer and file
buf = IOBuffer()
of = readwrite(outtrajfns[n], mode = "wb")
of = readwrite(outtrajfns[n], "wb")
# get frames
abs_temp_ind = np.argmin( abs(temps - outtemps[n]) )
@ -281,7 +282,7 @@ def write_reordered_traj(temp_inds, byte_inds, outtemps, temps,
def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
kB = 0.001987):
kB):
"""
Gets configurational log-weights (logw) for each frame and at each temp.
from the REMD simulation. ONLY WRITTEN FOR THE CANONICAL (NVT) ensemble.
@ -349,25 +350,25 @@ def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq,
#3) get reduced energies (*ONLY FOR THE CANONICAL ENSEMBLE*)
u_kln = np.zeros([ntemps, ntemps, nframes], float)
for k in range(ntemps):
for l in range(ntemps):
u_kln[ k, l, 0:nframes_k[k] ] = beta_k[l] * u_kn[k, 0:nframes_k[k]]
u_kln[k] = np.outer(beta_k, u_kn[k])
# run pymbar and extract the free energies
print("\nRunning pymbar...")
mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True)
f_k = mbar.f_k
f_k = mbar.f_k # (1 x k array)
# calculate the log-weights
print("\nExtracting log-weights...")
log_nframes = np.log(nframes)
logw = dict( (k, np.zeros([ntemps, nframes], float)) for k in range(ntemps) )
for l in range(ntemps):
# get log-weights to reweight to this temp.
for k in range(ntemps):
for n in range(nframes):
num = -beta_k[k] * u_kn[k,n]
denom = f_k - beta_k[k] * u_kn[k,n]
# get log-weights to reweight to this temp.
for k in range(ntemps):
for n in range(nframes):
num = -beta_k[k] * u_kn[k,n]
denom = f_k - beta_k[k] * u_kn[k,n]
for l in range(ntemps):
logw[l][k,n] = num - logsumexp(denom) - log_nframes
return logw
@ -516,8 +517,8 @@ if __name__ == "__main__":
comm.barrier()
# open all replica files for reading
infobjs = [readwrite(i) for i in intrajfns]
infobjs = [readwrite(i, "rb") for i in intrajfns]
# open all byteindex files
byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) )