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))
step = group.Reseeding(step1, reseed, maxnoimprove=maxnoimprove)
#save = pickle.load(open("storage"))
#save.nsave = 1000
save = savenlowest.SaveN(nsave=100, accuracy=1e-3)
save.compareMinima = dmagmin.compareMinima
opt = bh.BasinHopping(coords, pot, takeStep=step,
quenchRoutine=dmagmin.quenchCrystal,
temperature=temperature, storage=save,
quenchParameters=quenchParameters)
addColdFusionCheck(opt)
# create cif directory if it does not exist
import os, errno
try:
os.makedirs('cif')
except OSError, e:
if e.errno != errno.EEXIST:
raise
for i in xrange(1,nsteps/dump_frequency):
opt.run(dump_frequency)
#pickle.dump(save, open("storage."+str(i), "w"))
pickle.dump(save, open("storage", "w"))
i=0
for m in save.data:
i+=1
GMIN.writeCIF("cif/lowest%03d.cif"%(i), m.coords, "E"+str(m.energy))
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)
def compareMinima():
pass
if(options.writeCIF):
GMIN.initialize()
save = pickle.load(open(args[0]))
i=0
for m in save.data:
i+=1
print "minimum",i, "energy",m.E
if(options.writeCIF):
filename = options.cifDir+"/lowest%03d.cif"%(i)
print "writing",filename
GMIN.writeCIF(filename, m.coords, "E"+str(m.E))
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)
def compareMinima():
pass
if (options.writeCIF):
GMIN.initialize()
save = pickle.load(open(args[0]))
i = 0
for m in save.data:
i += 1
print "minimum", i, "energy", m.E
if (options.writeCIF):
filename = options.cifDir + "/lowest%03d.cif" % (i)
print "writing", filename
GMIN.writeCIF(filename, m.coords, "E" + str(m.E))