def get_compare_exact(self, **kwargs):
if self.pot.periodic:
permlist = self.get_permlist()
boxlengths = np.ones(3) * self.pot.boxl
measure = MeasurePeriodic(boxlengths, permlist)
return ExactMatchPeriodic(measure, accuracy=.1)
else:
return BLJCluster.get_compare_exact(self, **kwargs)
def get_compare_exact(self, **kwargs):
if self.pot.periodic:
permlist = self.get_permlist()
boxlengths = np.ones(3) * self.pot.boxl
measure = MeasurePeriodic(boxlengths, permlist)
return ExactMatchPeriodic(measure, accuracy=.1)
else:
return BLJCluster.get_compare_exact(self, **kwargs)
def start():
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster, BLJCluster
pl.ion()
natoms = 13
system = BLJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms, )
db = system.create_database() #dbname)
#get some minima
if True:
bh = system.get_basinhopping(database=db)
bh.run(20)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]
# only testing below here
#
def start():
wnd.start()
if __name__ == "__main__":
from OpenGL.GLUT import glutInit
import sys
import pylab as pl
app = QtGui.QApplication(sys.argv)
from pygmin.systems import LJCluster, BLJCluster
pl.ion()
natoms = 13
system = BLJCluster(natoms)
system.params.double_ended_connect.local_connect_params.NEBparams.iter_density = 5.
dbname = "lj%dtest.db" % (natoms,)
db = system.create_database()#dbname)
#get some minima
if True:
bh = system.get_basinhopping(database=db)
bh.run(20)
minima = db.minima()
else:
x1, e1 = system.get_random_minimized_configuration()[:2]
x2, e2 = system.get_random_minimized_configuration()[:2]
min1 = db.addMinimum(e1, x1)
min2 = db.addMinimum(e2, x2)
minima = [min1, min2]