Input:
coords.prmtop ( for number of atoms )
min.data, ts.data, extractedmin, extractedts
Output:
storage.sqlite
"""
# determine number of atoms from prmtop
prmtop = AmberPrmtopFile( 'coords.prmtop' ) # TOSET
natoms = prmtop.topology._numAtoms
# open database
db = Database(db="storage.sqlite") # TOSET
def read_coords(filee):
coords = np.zeros(3*natoms)
for i in xrange(natoms):
x = filee.readline().split()
coords[i*3:i*3+3] = [float(y) for y in x]
return coords
# counter to keep track of added minima
mini=1
minima={}
# for timing
tt = t0 = time.time()
step1 = takestep.AdaptiveStepsize(OXDNATakestep(displace=parameters.displace,
rotate=0.),
frequency=50)
step2 = takestep.AdaptiveStepsize(OXDNATakestep(displace=0.,
rotate=parameters.rotate),
frequency=50)
group.addBlock(100, step1)
group.addBlock(100, step2)
# with a generate random configuration
genrandom = OXDNAReseed()
# in a reseeding takestep procedure
reseed = takestep.Reseeding(group, genrandom, maxnoimprove=parameters.reseed)
# store all minima in a database
db = Database(db="storage.sqlite", accuracy=1e-2)
# create Basinhopping object
opt = BasinHopping(coords,
potential,
reseed,
db.minimum_adder(),
temperature=parameters.temperature)
# run for 100 steps
opt.run(parameters.nsteps)
# now dump all the minima
i = 0
for m in db.minima():
i += 1
def main():
# add some program options
parser = OptionParser(usage="usage: %prog [options] storage")
parser.add_option(
"--write-disconnect",
dest="writeDPS",
action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_option("-m",
dest="writeMinima",
action="store_true",
help="dump minima to screen")
parser.add_option("-t",
dest="writeTS",
action="store_true",
help="dump transition states to screen")
parser.add_option("--cif",
dest="writeCIF",
action="store_true",
help="export cif files")
parser.add_option("--cif-dir",
dest="cifDir",
default=".",
action="store",
type="string",
help="directory to write cifs to")
(options, args) = parser.parse_args()
# print help if no input file is given
if (len(args) != 1):
parser.print_help()
exit(-1)
db = Database(db=args[0])
if (options.writeMinima):
print "List of minima:"
print "---------------"
for m in db.minima():
print "%f\t\tid %d" % (m.energy, m._id)
print "END\n"
if (options.writeTS):
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if (options.writeDPS):
writeDPS(db)
if (options.writeCIF):
GMIN.initialize()
i = 0
for m in db.minima():
i += 1
filename = options.cifDir + "/lowest%03d.cif" % (i)
print "minimum", i, "energy", m.energy, "to", filename
GMIN.writeCIF(filename, m.coords, "E" + str(m.energy))
dumpcoords = False
opts, args = getopt.gnu_getopt(sys.argv[1:], "h",
["help", "dist", "dump-coords="])
for o, a in opts:
if o == "--dist":
printdist = True
elif o in ("-h", "--help"):
print usage
exit(1)
elif o == "--dump-coords":
dumpcoords = True
id = int(a)
else:
assert False, "unhandled option"
if len(args) == 0:
print usage
exit()
else:
dbfile = args[0]
database = Database(dbfile)
if dumpcoords:
printCoords(id, database)
exit(1)
if printe: printEnergies(database)
if printts: printTS(database)
if printdist: printDist(database)
