def create_basinhopping(self, **kwargs):
GMIN.initialize()
opt = AppClusterBH.create_basinhopping(self, **kwargs)
#self.database.compareMinima = compareMinima
opt.insert_rejected = True
addColdFusionCheck(opt)
return opt
def createBasinHopping(self):
GMIN.initialize()
pot = gminpot.GMINPotential(GMIN)
coords = pot.getCoords()
step = TestStep()
opt = bh.BasinHopping(coords, pot, takeStep=step, quenchRoutine=dmagmin.quenchCrystal, temperature=0.4, storage=self.storage)
addColdFusionCheck(opt)
return opt
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))
parser.add_option("-o","--out",
dest="out",# action="store",type="float",
help="store in this new object. If not given, the input file is overwritten")
(options, args) = parser.parse_args()
# print help if no input file is given
if(len(args) != 1):
parser.print_help()
exit(-1)
infile = args[0]
outfile = infile
# initialize GMIN
GMIN.initialize()
pot = gminpotential.GMINPotential(GMIN)
crystals.GMIN = GMIN
# open the storage class
db_in = Database(db=infile)
if(options.out!=None):
outfile = options.out
db_out = Database(db=outfile)
print "Start to reoptimize minima"
for m in db_in.minima():
print "optimizing minima",m._id,", energy", m.energy
ret = dmagmin.quenchCrystal(m.coords, pot.getEnergyGradient, tol=options.tol, maxErise=options.maxErise)
print "new energy",ret[1],"(difference %f)"%(ret[1] - m.energy)
print
def __init__(self):
self.storage = savenlowest.SaveN(10)
GMIN.initialize()
defaults.quenchRoutine = dmagmin.quenchCrystal
defaults.quenchParams["tol"]=1e-4
