def dosimul(zoom, build = True):
global fncfg, fnout, cmdopt
# build the program
progdir = "../prog/lj"
if not os.path.isdir(progdir):
progdir = "../" + progdir
if build:
zcom.runcmd("make -C %s" % progdir)
prog = "md"
try:
# make a copy of the program in case
# it gets modified or deleted later
shutil.copy("%s/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd = "./%s -t%s -Z%s %s" % (prog, nsteps, zoom, cmdopt)
if dKdE > 0: cmd += " -G%s" % dKdE
if Etot != None: cmd += " -E%s" % Etot
if Edev != None: cmd += " -D%s" % Edev
cmd = cmd.strip()
fnlog = "ez%s.log" % zoom
ln = "# zoom %s, nsteps %s, dKdE %s, Etot %s, Edev %s\n" % (
zoom, nsteps, dKdE, Etot, Edev)
open(fnlog, "w").write(ln) # empty the log
print "CMD: %s; LOG %s" % (cmd, fnlog)
cnt = 0
esum = 0
e2sum = 0
eisum = 0
ei2sum = 0
for i in range(ntrials):
ret, out, err = zcom.runcmd(cmd, capture = True, verbose = 0)
# get the last line of the output
result = err.strip().split('\n')[-1]
etot, etav, eitot = geterror(result)
# print results
cnt += 1
eisum += eitot
ei2sum += eitot * eitot
eiave = eisum / cnt
eivar = ei2sum / cnt - eiave * eiave
esum += etot
e2sum += etot * etot
eave = esum / cnt
evar = e2sum / cnt - eave * eave
print "count %s, total energy %s, ave %s, var %s, init %s, iave %s, ivar %s" % (
cnt, etot, eave, evar, eitot, eiave, eivar)
ln = "%d %s %s %s\n" % (cnt, etot, eitot, etav)
open(fnlog, "a").write(ln)
return cnt, eave, evar, eiave, eivar
def main():
global cmdopt, fnlog
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/lj" % progdir)
if doev:
prog = "ljwham2"
if not fnlog: fnlog = "lj2.log"
hisopt = "--fnhis2"
fnhis = "hist2.dat"
else:
prog = "ljwham"
if not fnlog: fnlog = "lj.log"
hisopt = "--fnhis"
fnhis = "hist.dat"
arr = os.path.splitext(fnlog)
fntmlog = arr[0] + "tm" + arr[1]
fnhis = arr[0] + "_" + fnhis
try:
shutil.copy("%s/lj/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s %s=%s %s %s" % (
prog, hisopt, fnhis, tol, cmdopt)
cmd0 = cmd0.strip()
ns = [0]*(nbases + 1)
tm = [0]*(nbases + 1)
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
cmd = "%s --re %s %s" % (cmd0, nequil, nsteps)
ret, out, err = zcom.runcmd(cmd.strip(), capture = True)
ns[0], tm[0] = getnstepstime(err)
for nb in range(1, nbases + 1):
cmd = "%s --wham=MDIIS --nbases=%d -H %s %s" % (
cmd0, nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture = True)
ns[nb], tm[nb] = getnstepstime(err)
# save to the log files
open(fnlog, "a").write(" ".join(ns) + "\n")
open(fntmlog, "a").write(" ".join(tm) + "\n")
def main():
global cmdopt, fnlog
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/lj" % progdir)
if doev:
prog = "ljwham2"
if not fnlog: fnlog = "lj2.log"
hisopt = "--fnhis2"
fnhis = "hist2.dat"
else:
prog = "ljwham"
if not fnlog: fnlog = "lj.log"
hisopt = "--fnhis"
fnhis = "hist.dat"
arr = os.path.splitext(fnlog)
fntmlog = arr[0] + "tm" + arr[1]
fnhis = arr[0] + "_" + fnhis
try:
shutil.copy("%s/lj/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s %s=%s %s %s" % (prog, hisopt, fnhis, tol, cmdopt)
cmd0 = cmd0.strip()
ns = [0] * (nbases + 1)
tm = [0] * (nbases + 1)
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
cmd = "%s --re %s %s" % (cmd0, nequil, nsteps)
ret, out, err = zcom.runcmd(cmd.strip(), capture=True)
ns[0], tm[0] = getnstepstime(err)
for nb in range(1, nbases + 1):
cmd = "%s --wham=MDIIS --nbases=%d -H %s %s" % (
cmd0, nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture=True)
ns[nb], tm[nb] = getnstepstime(err)
# save to the log files
open(fnlog, "a").write(" ".join(ns) + "\n")
open(fntmlog, "a").write(" ".join(tm) + "\n")
def getprogdir(build = True):
''' find the directory of NAMD '''
global progdir
if not progdir:
progdir = "../../NAMD_mods/NAMD_2.11_thstat/Linux-x86_64-g++"
i = 0
while not os.path.isdir(progdir):
progdir = "../" + progdir
i += 1
if i > 3: break
if build: # build the program
zcom.runcmd("make -C %s" % progdir)
return progdir
def mkpdb(fnpdb, doext, angs, ter):
''' copy PDB to the running directory '''
# 1. copy or download the input pdb into the working directory
if os.path.exists(fnpdb):
# copy `fnpdb' to the current directory
fnpdb0 = os.path.basename(fnpdb)
shutil.copy2(fnpdb, fnpdb0)
print "copying %s to %s" % (fnpdb, fnpdb0)
fnpdb = fnpdb
else:
# `fnpdb' is the standard 4-letter PDB code
if not fnpdb.endswith(".pdb") and len(fnpdb) == 4:
fnpdb = fnpdb.upper() + ".pdb"
# try to download from RCSB
if zcom.runcmd("wget http://www.rcsb.org/pdb/files/" + fnpdb,
system = True)[0] != 0:
print "cannot download", fnpdb
raise Exception
# 2. create an extended configuration
if doext:
fnpdbx = "out.pdb"
import mkspx
seq = mkspx.pdb2seq(fnpdb)
src = mkspx.mkpdb(seq, angs, ter, False, gmxver)
print("saving the extended configuration to " + fnpdbx)
open(fnpdbx, "w").write(src)
fnpdb = fnpdbx
# 3. renumber residues from 1
fnpdb = renumpdb(fnpdb)
return fnpdb
def main():
global radd, cmdopt, fnls, fntr
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/gmx" % progdir)
if doev:
prog = "xvgwham2"
if not fntr: fntr = "xvg2.tr"
if not fnls: fnls = "ev.ls"
fnhis = "hist2.dat"
else:
prog = "xvgwham"
if not fntr: fntr = "xvg.tr"
if not fnls: fnls = "e.ls"
fnhis = "hist.dat"
arr = os.path.splitext(fntr)
fnhis = arr[0] + "_tr_" + fnhis
try:
shutil.copy("%s/gmx/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s -v --fnhis=%s -r %g %s %s %s %s %s" % (
prog, fnhis, radd, fnls, itmin, itmax, tol, cmdopt)
cmd0 = cmd0.strip()
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
ret, out, err = zcom.runcmd(cmd, capture=True)
gettrace(0, err)
for nb in range(dnbases, nbases + 1, dnbases):
cmd = "%s --wham=MDIIS --nbases=%d -H %s %s" % (
cmd0, nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture=True)
gettrace(nb, err)
def main():
global cmdopt, fntr
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/is2" % progdir)
prog = "is2wham"
arr = os.path.splitext(fntr)
fnhis = arr[0] + "_tr_hist.dat"
try:
shutil.copy("%s/is2/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s -v --fnhis=%s %s %s %s %s" % (prog, fnhis, itmin, itmax, tol,
cmdopt)
cmd0 = cmd0.strip()
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
cmd = "%s --re %s %s" % (cmd0, nequil, nsteps)
ret, out, err = zcom.runcmd(cmd, capture=True)
gettrace(0, err)
for nb in range(dnbases, nbases + 1, dnbases):
cmd = "%s --wham=MDIIS --nbases=%d -H %s %s" % (
cmd0, nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture=True)
gettrace(nb, err)
def main():
global cmdopt, fntr
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/is2" % progdir)
prog = "is2wham"
arr = os.path.splitext(fntr)
fnhis = arr[0] + "_tr_hist.dat"
try:
shutil.copy("%s/is2/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s -v --fnhis=%s %s %s %s %s" % (
prog, fnhis, itmin, itmax, tol, cmdopt)
cmd0 = cmd0.strip()
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
cmd = "%s --re %s %s" % (cmd0, nequil, nsteps)
ret, out, err = zcom.runcmd(cmd, capture = True)
gettrace(0, err)
for nb in range(dnbases, nbases + 1, dnbases):
cmd = "%s --wham=MDIIS --nbases=%d -H %s %s" % (
cmd0, nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture = True)
gettrace(nb, err)
def runmd(fningro, fnout, fnmdp, fntop, pd, capture):
''' run mdrun with the structure in `fningro' '''
if fnout.endswith(".gro"):
fnout = os.path.splitext(fnout)[0]
ret = gmxshrun(grompp + " -v -f " + fnmdp + " -o " + fnout + ".tpr "
+ "-c " + fningro + " -p " + fntop + " -maxwarn 5",
capture)
print "\n\nRunning mdrun with %s, may take some time..." % fnout
cmd = mdrun + " -v -deffnm " + fnout
# if `ns_type' is `simple' instead of `grid'
# we have to use particle decomposition
if pd: cmd += " -pd"
ret = zcom.runcmd(cmd, capture)
zcom.die_if(ret[0] != 0, "mdrun failed with %s" % fnout)
return fnout + ".gro"
def scan():
global fncfg, fnout, cmdopt
progdir = "../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
# build the program
zcom.runcmd("make -C %s" % progdir)
prog = "invt"
try:
# make a copy of the program in case
# it gets modified or deleted later
shutil.copy("%s/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s %s %s" % (prog, fncfg, cmdopt)
cmd0 = cmd0.strip()
# create a table of c-values
cval = []
if sigscan:
sig = sigmin
while sig < sigmax + sigdel * 0.01:
cval += [ sig, ]
sig += sigdel
srange = "sig=%s:%s:%s" % (sigmin, sigdel, sigmax)
varname = "Gaussian sigma"
elif okscan:
ok = okmin
while ok < okmax + okdel * 0.01:
cval += [ ok, ]
ok += okdel
srange = "ok=%s:%s:%s" % (okmin, okdel, okmax)
varname = "bandpass cutoff K"
elif ikscan:
ik = ikmin
okold = -1
while ik < ikmax + ikdel * 0.01:
ok = int(ikconst / ik + 0.5)
if ok != okold: # avoid redundancy
cval += [ ok, ]
ik += ikdel
okold = ok
srange = "ik=%s:%s:%s" % (ikmin, ikdel, ikmax)
varname = "inverse bandpass cutoff K"
elif iascan:
ia = iamin
iafac = 10.0 ** iadel
while ia < iamax * iafac:
cval += [ ia, ]
ia *= iafac
srange = "ia=%s:%s:%s" % (iamin, iadel, iamax)
varname = "initial updating magnitude, alpha(0)"
else:
raise
# we save data to a temporary file
# and overwrite the actual file only at the end
if os.path.exists(fnout):
fnouttmp = fnout + ".tmp"
else:
fnouttmp = fnout
# text of the output
txt = ""
# print out an information line
sinfo = "# %s %s %s\n" % (fncfg, cmdopt, srange)
txt += sinfo
# go over the predefined c-values
for i in range(len(cval)):
print "%d: testing for %s value %s..." % (
i, varname, cval[i])
c = cval[i]
if sigscan:
cmd = "%s --sig=%s" % (cmd0, c)
elif okscan or ikscan:
cmd = "%s --okmax=%s" % (cmd0, c)
elif iascan:
cmd = "%s --opta --inita=%s" % (cmd0, c)
else:
raise
ret, out, err = zcom.runcmd(cmd.strip(), capture = True)
e, ei, enorm, stde, stdei = geterror(out)
# construct a line of output
s = "%s\t%s\t%s\t%s\t%s\t%s\n" % (
c, e, ei, enorm, stde, stdei)
txt += s
# save to the output file
open(fnouttmp, "w").write(txt)
# write the entire text at the end
# we do not trust the content of fnouttmp,
# which is only for backup, and may have been changed
open(fnout, "w").write(txt)
# remove the temporary file
if fnouttmp != fnout:
os.remove(fnouttmp)
def main():
global bootstrap, est, mbar, cmdopt, fnls, fnlog
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/gmx" % progdir)
if doev:
if mbar:
prog = "xvgmbar2"
else:
prog = "xvgwham2"
if not fnlog: fnlog = "xvg2err.log"
if not fnls: fnls = "ev.ls"
hisopt = "--fnhis2"
fnhis = "histerr2.dat"
else:
if mbar:
prog = "xvgmbar"
else:
prog = "xvgwham"
if not fnlog: fnlog = "xvgerr.log"
if not fnls: fnls = "e.ls"
hisopt = "--fnhis"
fnhis = "histerr.dat"
if mbar:
strfnhis = ""
# modify the the log file name
arr = os.path.splitext(fnlog)
if not est:
fnlog = arr[0] + "_mbar" + arr[1]
else:
arr = os.path.splitext(fnlog)
wmethod = whammethod.upper()
if wmethod.startswith("UI"):
method = "ui"
elif wmethod == "ST":
method = "st"
else:
method = ""
fnlog = arr[0] + "_wham" + method + arr[1]
fnhis = arr[0] + method + "_" + fnhis
strfnhis = hisopt + "=" + fnhis
try:
shutil.copy("%s/gmx/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s -v %s %s %s %s %s %s --%s=%s %s %s" % (
prog, strfnhis, fnls, cmdopt, radd, bootstrap,
"--est" if est else "",
"mbar" if mbar else "wham", whammethod, nbases,
strfnact)
cmd0 = cmd0.strip()
if bootstrap and not mbar:
# run for the first time to save the histogram
zcom.runcmd(cmd0)
# we will load the histogram, and bootstrap later on
cmd0 += " -H"
if est:
arr = os.path.splitext(fnlog)
fnlogs = [
arr[0] + "avea_mbar" + arr[1],
arr[0] + "aveb_mbar" + arr[1],
arr[0] + "avec_mbar" + arr[1],
arr[0] + "expa_mbar" + arr[1],
arr[0] + "expb_mbar" + arr[1],
arr[0] + "bar_mbar" + arr[1],
arr[0] + "gp_mbar" + arr[1],
arr[0] + "tg_mbar" + arr[1],
arr[0] + "lnv_mbar" + arr[1],
]
else:
fnlogs = [ fnlog ]
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# run WHAM
ret, out, err = zcom.runcmd(cmd0.strip(), capture = True)
if i == 0:
bet = getcol(out, 1)
hdr = "#HEADER " + " ".join(bet) + "\n"
for fnlog in fnlogs:
open(fnlog, "a").write(hdr)
for i in range(len(fnlogs)):
fnlog = fnlogs[i]
col = i + 2
lnz = getcol(out, col)
open(fnlog, "a").write(" ".join(lnz) + "\n")
elif o in ("--verbose",):
verbose = int(a)
elif o in ("-t", "-T",):
temp = float(a)
elif o in ("-p", "-P",):
pres = float(a)
elif o in ("-m",):
nequil = int(a)
elif o in ("-n",):
nsteps = int(a)
elif o in ("--nt",):
nthreads = int(a)
elif o in ("-h", "--help"):
usage()
ret, out, err = zcom.runcmd("uname -a", capture = True)
if out.find("host.utmb.edu") >= 0:
srcroot = "$HOME/lwork/gmx/gromacs5.0"
buildroot = srcroot + "/buildgccdbl"
gmxtopdir = srcroot + "/share/top"
def changensteps(fn, nsteps):
''' set the number of steps in the .mdp file '''
s = open(fn).readlines()
for i in range(len(s)):
if s[i].startswith("nsteps"):
s[i] = "nsteps = %d\n" % nsteps
open(fn, "w").writelines(s)
def dotrace(zoom, build = True, fntrace = None):
global fncfg, nsteps, cmdopt, Etot, Edev
global thermostat, tNHCPeriod, langRescaleDt
progdir = getprogdir(build)
if Edev == None: Edev = 100
if Etot == None: Etot = -6141.16
Etot += Edev
Edev = 0
# copy files from the source directory
fnpsf, fnpdb, fnprm, scfg = getfiles("normal")
# create a temporary directory
rundir = "tmprun"
if not os.path.exists(rundir):
os.mkdir(rundir)
# move to the running directory
os.chdir(rundir)
# program directory
prog = "../" + progdir + "/namd2 +p%s" % nproc
# copy files
os.system("cp %s ." % fnpsf)
os.system("cp %s ." % fnpdb)
os.system("cp %s ." % fnprm)
if nsteps == None: nsteps = 1
# command line
fncfg = "run.conf"
cmd = "%s %s %s" % (prog, cmdopt, fncfg)
# output file
if not fntrace: fntrace = "etot.tr"
fntrace = "../" + fntrace
# construct a configuration file
fnene = "ene0.log"
strcfg = scfg + '''
energyLogFile %s
energyLogFreq 1
energyLogTotal on
''' % (fnene)
if not thermostat:
strcfg += '''
rescaleAdaptive on
rescaleAdaptiveZoom %s
rescaleAdaptiveFileFreq 1000
''' % (zoom)
if dKdE > 0:
strcfg += "rescaleAdaptiveDKdE %s\n" % dKdE
elif thermostat == "NH":
# Nose-Hoover thermostat
strcfg += '''
tNHC on
tNHCTemp $temperature
tNHCLen 5
tNHCPeriod %g
''' % (tNHCPeriod)
elif thermostat.startswith("VR"):
# Langevin-style velocity rescaling
strcfg += '''
langRescale on
langRescaleTemp $temperature
langRescaleDt %g
''' % (langRescaleDt)
else: # if thermostat.startswith("L"):
# Langevin thermostat
strcfg += '''
langevin on
langevinDamping 1
langevinTemp $temperature
'''
if Etot != None:
strcfg += "rescaleInitTotal %s\n" % Etot
if Edev != None:
strcfg += "rescaleInitDev %s\n" % Edev
strcfg += "run %s\n" % nsteps
open(fncfg, "w").write(strcfg)
print "CMD: %s; TRACE %s; CFG %s" % (cmd, fntrace, fncfg)
eparr = []
ekarr = []
etarr = []
# multiple trials
i = 0
while i < ntrials:
# clear the directory
os.system("rm -rf *.dat *.BAK *.old ene*.log *.vel *.xsc *.xst *.coor")
ret, out, err = zcom.runcmd(cmd, capture = True, verbose = 0)
# extract the energy
ss = open(fnene).read().strip().split('\n')
ssplit = [ln.strip().split() for ln in ss]
tm = len(ss)
# initialize the accumulators
if i == 0:
etarr = [ Ave() for k in range(tm) ]
eparr = [ Ave() for k in range(tm) ]
ekarr = [ Ave() for k in range(tm) ]
if os.path.exists(fntrace): # load previous record
s = open(fntrace).readlines()
tags = s[0].split()
cnt = int( tags[2][:-1] )
fzoom = float( tags[4][:-1] )
nsteps = int( tags[6][:-1] )
if nsteps != tm - 1: # loading previous data
print "previous nsteps %s is not %s" % (nsteps, tm - 1)
else:
for k in range(tm):
arr = [float(x) for x in s[k+1].split()]
etarr[k].load(cnt, arr[1], arr[2])
eparr[k].load(cnt, arr[3], arr[4])
ekarr[k].load(cnt, arr[5], arr[6])
i = cnt
# update the accumulators for the total, potential and kinetic energies
for k in range(tm):
epot = float( ssplit[k][1] )
eparr[k].add(epot)
etot = float( ssplit[k][2] )
etarr[k].add(etot)
ekin = etot - epot
ekarr[k].add(ekin)
print "count %s, total energy, final: ave %s, fvar %s, init: ave %s, var %s" % (
i + 1, etarr[-1].getave(), etarr[-1].getvar(),
etarr[0].getave(), etarr[0].getvar())
strace = "# count %s, zoom %s, nsteps %s, dKdE %s, Etot %s, Edev %s\n" % (
etarr[0].n, zoom, nsteps, dKdE, Etot, Edev)
# output the trace file
for k in range(tm):
strace += "%s\t%g\t%g\t%g\t%g\t%g\t%g\n" % ( ssplit[k][0],
etarr[k].getave(), etarr[k].getvar(),
eparr[k].getave(), eparr[k].getvar(),
ekarr[k].getave(), ekarr[k].getvar() )
open(fntrace, "w").write(strace)
i += 1
# go back to the parent directory
os.chdir("..")
shutil.copy2(phony, fnm)
def restore_orig(files):
for fnm in files:
fnmbak=fnm+'b'
print "Restoring the original "+fnm
os.rename(fnmbak, fnm)
devver=False
# this is the folder where the script resides, not where we run it
# mypath=sys.path[0]
runpath=os.getcwd()
#print mypath, mypath.find("gromacs-4.0."),os.getcwd()
if (runpath.find("gmxgit") >= 0 or
runpath.find("gromacs-4.0.") >=0): devver=True
if not devver:
print "This is not a testing system, do you really want to continue?"
if raw_input().startswith("n"): exit(1);
create_phony(['Makefile.am', 'Makefile.in'])
runcmd(['tar', 'cvphzf', target]+prune_filelist(filelist))
if not devver:
restore_orig(['Makefile.am', 'Makefile.in'])
print "%s size %d" %(target, len(open(target).read()))
runcmd(['gnome-open',target])
def main():
global mbar, radd, cmdopt, fnls, fnlog, fnact
progdir = "../../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
zcom.runcmd("make -C %s/gmx" % progdir)
if doev:
if mbar:
prog = "xvgmbar2"
else:
prog = "xvgwham2"
if not fnlog: fnlog = "xvg2.log"
if not fnls: fnls = "ev.ls"
hisopt = "--fnhis2"
fnhis = "hist2.dat"
else:
if mbar:
prog = "xvgmbar"
else:
prog = "xvgwham"
if not fnlog: fnlog = "xvg.log"
if not fnls: fnls = "e.ls"
hisopt = "--fnhis"
fnhis = "hist.dat"
if mbar:
strfnhis = ""
# modify the the log file name
arr = os.path.splitext(fnlog)
fnlog = arr[0] + "_mbar" + arr[1]
else:
arr = os.path.splitext(fnlog)
fnlog = arr[0] + "_wham" + arr[1]
fnhis = arr[0] + "_" + fnhis
strfnhis = hisopt + "=" + fnhis
arr = os.path.splitext(fnlog)
fntmlog = arr[0] + "tm" + arr[1]
try:
shutil.copy("%s/gmx/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s %s %s %s %s %s" % (
prog, strfnhis, fnls, tol, fnact, cmdopt)
cmd0 = cmd0.strip()
if radd < 1:
cmd0 += " -r %g" % radd
if not mbar:
# run for the first time to save the histogram
zcom.runcmd(cmd0 + " --wham=ST")
# we will load the histogram, and bootstrap later on
cmd0 += " --bootstrap -H"
else:
# no need to bootstrap if only a random subsample is used
if radd >= 1:
cmd0 += " --bootstrap"
cmd0 = cmd0.strip()
ns = [0]*(nbases + 1)
tm = [0]*(nbases + 1)
for i in range(nsamp):
print "running sample %d/%d..." % (i, nsamp)
# use the direct WHAM
ret, out, err = zcom.runcmd(cmd0, capture = True)
ns[0], tm[0] = getnstepstime(err)
for nb in range(1, nbases + 1):
cmd = "%s --%s=MDIIS --nbases=%d %s %s" % (
cmd0, "mbar" if mbar else "wham",
nb, update_method, mthreshold)
ret, out, err = zcom.runcmd(cmd.strip(), capture = True)
ns[nb], tm[nb] = getnstepstime(err)
# save to the log files
open(fnlog, "a").write(" ".join(ns) + "\n")
open(fntmlog, "a").write(" ".join(tm) + "\n")
temp = float(a)
elif o in (
"-p",
"-P",
):
pres = float(a)
elif o in ("-m", ):
nequil = int(a)
elif o in ("-n", ):
nsteps = int(a)
elif o in ("--nt", ):
nthreads = int(a)
elif o in ("-h", "--help"):
usage()
ret, out, err = zcom.runcmd("uname -a", capture=True)
if out.find("host.utmb.edu") >= 0:
srcroot = "$HOME/lwork/gmx/gromacs5.0"
buildroot = srcroot + "/buildgcc"
gmxtopdir = srcroot + "/share/top"
def changensteps(fn, nsteps):
''' set the number of steps in the .mdp file '''
s = open(fn).readlines()
for i in range(len(s)):
if s[i].startswith("nsteps"):
s[i] = "nsteps = %d\n" % nsteps
open(fn, "w").writelines(s)
def dosimul(zoom, build = True, fnlog = None):
global fncfg, nsteps, cmdopt, Etot, Edev
progdir = getprogdir(build)
# copy files from the source directory
fnpsf, fnpdb, fnprm, scfg = getfiles("normal")
# create a temporary directory
rundir = "tmprun"
if not os.path.exists(rundir):
os.mkdir(rundir)
# move to the running directory
os.chdir(rundir)
# program directory
prog = "../" + progdir + "/namd2 +p%s" % nproc
# copy files
os.system("cp %s ." % fnpsf)
os.system("cp %s ." % fnpdb)
os.system("cp %s ." % fnprm)
if nsteps == None: nsteps = 1000
# command line
fncfg = "run.conf"
cmd = "%s %s %s" % (prog, cmdopt, fncfg)
# output file
if not fnlog: fnlog = "ez%s_t%s.log" % (zoom, nsteps)
fnlog = "../" + fnlog
ln = "# zoom %s, nsteps %s, dKdE %s, Etot %s, Edev %s\n" % (
zoom, nsteps, dKdE, Etot, Edev)
open(fnlog, "a").write(ln)
print "CMD: %s; LOG %s" % (cmd, fnlog)
ef = Ave()
ei = Ave()
# multiple trials
for i in range(ntrials):
# write the configuration file
fnene = "ene0.log"
strcfg = scfg + '''
rescaleAdaptive on
rescaleAdaptiveZoom %s
rescaleAdaptiveFileFreq 1000
energyLogFile %s
energyLogFreq 10
energyLogTotal on
''' % (zoom, fnene)
if dKdE > 0:
strcfg += "rescaleAdaptiveDKdE %s\n" % dKdE
if Etot != None:
strcfg += "rescaleInitTotal %s\n" % Etot
if Edev != None:
strcfg += "rescaleInitDev %s\n" % Edev
strcfg += "run %s\n" % nsteps
open(fncfg, "w").write(strcfg)
# clear the directory
os.system("rm -rf *.dat *.BAK *.old ene*.log *.vel *.xsc *.xst *.coor")
ret, out, err = zcom.runcmd(cmd, capture = True, verbose = 0)
# extract the energy
ss = open(fnene).readlines()
eitot = float( ss[0].split()[2] )
j = -1
while ss[j].strip() == "":
j -= 1
etot = float( ss[j].split()[2] )
# update accumulators and print results
ei.add(eitot)
ef.add(etot)
print "count %s, total energy %s, ave %s, var %s, init %s, iave %s, ivar %s" % (
ef.n, etot, ef.getave(), ef.getvar(), eitot, ei.getave(), ei.getvar())
ln = "%d %s %s\n" % (ef.n, etot, eitot)
open(fnlog, "a").write(ln)
# go back to the parent directory
os.chdir("..")
return ef.n, ef.getave(), ef.getvar(), ei.getave(), ei.getvar()
def c_scan():
global fncfg, fnout, fnprd, cmdopt, fnout
progdir = "../prog"
if not os.path.isdir(progdir):
progdir = "../" + progdir
# build the program
zcom.runcmd("make -C %s" % progdir)
prog = "invt"
try:
# make a copy of the program in case
# it gets modified or deleted later
shutil.copy("%s/%s" % (progdir, prog), "./%s" % prog)
except:
pass
cmd0 = "./%s %s %s" % (prog, fncfg, cmdopt)
cmd0 = cmd0.strip()
# create a table of c-values
cval = []
if cscan:
# linear c values
c = cmin
while c < cmax + cdel * 0.01:
cval += [c]
c += cdel
srange = "c=%s:%s:%s" % (cmin, cdel, cmax)
# construct the larger range for the analytical prediction
if cmin > cdel:
cmin1 = cmin - cdel
else:
cmin1 = 0
cmax1 = cmax + cdel
elif lscan:
# linear l values, c = 1/l
l = lmin
while l < lmax + ldel * 0.01:
cval += [1.0 / l]
l += ldel
srange = "lambda=%s:%s:%s" % (lmin, ldel, lmax)
# construct the larger range for the analytical prediction
cmin1 = 1 / (lmax + ldel)
if lmin > ldel:
cmax1 = 1 / (lmin - ldel)
else:
cmax1 = 1 / lmin
elif xscan:
# logarithm c vales
logc = log(xmin)
dlogc = xdel * log(10)
while logc < log(xmax) + dlogc * 0.01:
cval += [exp(logc)]
logc += dlogc
srange = "x=%s:%s:%s" % (xmin, xdel, xmax)
cmin1 = xmin
cmax1 = xmax
dc1 = 0.01
if cmin1 <= 0:
cmin1 = dc1
# generate the prediction result
os.system(
"%s/predict %s %s --cmin=%s --cdel=%s --cmax=%s > %s" % (progdir, fncfg, cmdopt, cmin1, dc1, cmax1, fnprd)
)
# we save data to a temporary file
# and overwrite the actual file only at the end
if os.path.exists(fnout):
fnouttmp = fnout + ".tmp"
else:
fnouttmp = fnout
# text of the output
txt = ""
# print out an information line
sinfo = "# %s %s %s\n" % (fncfg, cmdopt, srange)
txt += sinfo
# go over the predefined c-values
for i in range(len(cval)):
print "%d: testing for c-value %s..." % (i, cval[i])
c = cval[i]
# override the c value
cmd = "%s -c %s" % (cmd0, c)
ret, out, err = zcom.runcmd(cmd.strip(), capture=True)
e, ei, stde, stdei = geterror(out)
# construct a line of output
s = "%s\t%s\t%s\t%s\t%s\n" % (c, e, ei, stde, stdei)
txt += s
# save to the output file
open(fnouttmp, "w").write(txt)
# write the entire text at the end
# we do not trust the content of fnouttmp,
# which is only for backup, and may have been changed
open(fnout, "w").write(txt)
# remove the temporary file
if fnouttmp != fnout:
os.remove(fnouttmp)