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 __init__(self, natoms, boxvec, rho=2., r0=1., A=1., rcut=None):
super(MorseBulk, self).__init__(natoms, rho=rho, r0=r0, A=A, rcut=rcut)
self.boxvec = boxvec
self.periodic = True
self.params.double_ended_connect.local_connect_params.NEBparams.interpolator = InterpolateLinearMeasure(
MeasurePeriodic(self.boxvec))
def __init__(self, natoms, boxvec, ntypeA="default", **potential_kwargs):
super(BLJBulk, self).__init__(natoms,
ntypeA=ntypeA,
**potential_kwargs)
self.boxvec = np.array(boxvec)
self.periodic = True
self.potential_kwargs["boxvec"] = self.boxvec
self.params.double_ended_connect.local_connect_params.NEBparams.interpolator = InterpolateLinearMeasure(
MeasurePeriodic(self.boxvec))
def setUp(self):
self.natoms = 100
rho = .5
boxl = (float(self.natoms) / rho)**(1. / 3)
boxlengths = np.ones(3) * boxl + np.random.rand(3) * .1
self.permlist = self.get_permlist()
self.measure = MeasurePeriodic(boxlengths, self.permlist)
self.x1 = self.get_random_configuration()
self.x2diff = self.get_random_configuration()
self.x2same = self.randomly_permute(self.x1.copy())
self.exact_match = ExactMatchPeriodic(self.measure, accuracy=1e-5)
def __init__(self, radii, boxvec, power=2):
super(SoftSphereSystem, self).__init__(self)
self.radii = np.array(radii)
self.natoms = self.radii.size
self.boxvec = np.array(boxvec)
self.periodic = True
self.potential_kwargs = dict()
self.power = power
self.eps = 1.
self.set_params(self.params)
self.params.double_ended_connect.local_connect_params.NEBparams.interpolator = InterpolateLinearMeasure(
MeasurePeriodic(self.boxvec))
def setUp(self):
self.nrigid = 5
self.boxl = np.array([5, 5, 5])
self.system = MorseBulk(self.nrigid, self.boxl)
# self.mindist = self.system.get_mindist()
self.transform = TransformPeriodic()
self.measure = MeasurePeriodic(self.boxl, permlist=[])
self.exact_match = ExactMatchPeriodic(self.measure, accuracy=1e-5)
self.mindist = MinDistBulk(self.boxl, self.measure)
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
self.x2same = self.x1.copy()
self.x2trans = self.x1.copy()
trans = np.random.random(3) * self.boxl
self.transform.translate(self.x2trans, trans)
def test1(self):
natoms = 10
L = 4.
boxvec = np.ones(3) * L
xi = np.random.uniform(0, L, 3 * natoms)
xf = np.random.uniform(0, L, 3 * natoms)
measure = MeasurePeriodic(boxvec)
dist = measure.get_dist(xi, xf)
int = InterpolateLinearMeasure(measure)
for f in [0, .1, .2, .3, .8, .9, 1]:
x3 = int(xi, xf, f)
d2 = measure.get_dist(xi, x3)
self.assertAlmostEqual(f * dist, d2)
def get_compare_exact(self):
accuracy = self.params.database.accuracy
measure = MeasurePeriodic(self.boxvec, self.get_permlist())
compare = ExactMatchPeriodic(measure, accuracy=accuracy)
return compare
def get_compare_exact(self):
accuracy = 1e-2
measure = MeasurePeriodic(self.boxvec, self.get_permlist())
compare = ExactMatchPeriodic(measure, accuracy=accuracy)
return compare
def get_mindist(self):
measure = MeasurePeriodic(self.boxvec, permlist=self.get_permlist())
return MinDistBulk(self.boxvec, measure)
