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 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 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 __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 get_compare_exact(self):
accuracy = self.params.database.accuracy
measure = MeasurePeriodic(self.boxvec, self.get_permlist())
compare = ExactMatchPeriodic(measure, accuracy=accuracy)
return compare
class TestExactMatchPeriodic(unittest.TestCase):
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 randomly_permute(self, x):
import random
x = x.reshape(-1, 3)
xnew = x.copy()
for atomlist in self.permlist:
permutation = copy.copy(atomlist)
random.shuffle(permutation)
xnew[atomlist, :] = x[permutation, :]
return xnew.flatten()
def test_exact_match(self):
self.assertTrue(self.exact_match(self.x1, self.x2trans))
def test_no_exact_match(self):
self.assertFalse(self.exact_match(self.x1, self.x2diff))
def test_exact_match_periodic(self):
self.x2same[:3] += self.boxl
self.assertTrue(self.exact_match(self.x1, self.x2same))
# This test is pretty superfluous for the atomic-system case. But it doesn't take long and probably
# doesn't hurt.
def test_align_translate(self):
np.random.seed(4)
n = self.nrigid
fail_counter = 0
for i in range(10000):
# if (i%100 == 0):
# print i
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
try:
dist, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
pass
if self.exact_match(self.x2diff, x2) is False:
fail_counter += 1
self.assertFalse(fail_counter,
"bond lengths were changed %d times" % fail_counter)
def test_align_match(self):
np.random.seed(2)
fail_counter = 0
for i in range(1):
# if (i%100 == 0):
# print i
self.x1 = self.system.get_random_configuration()
self.x2trans = self.x1
translate = np.random.random(3) * self.boxl
self.transform.translate(self.x2trans, translate)
try:
dist, x1, x2 = self.mindist(self.x1, self.x2trans)
except RuntimeError:
pass
if (dist > 1e-5):
fail_counter += 1
print(dist)
self.assertFalse(fail_counter,
"structure matching failed %d times" % fail_counter)
def test_align_permutation(self):
np.random.seed(4)
fail_counter = 0
for i in range(1):
if (i % 100 == 0):
print(i)
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
try:
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
fail_counter += 1
self.assertFalse(fail_counter,
"rotational alignment failed %d times" % fail_counter)
def test_align_improvement(self, verbose=True):
np.random.seed(6)
max_step = 10000
fail_counter = 0
ave = 0
ave_inc = 0
for i in range(max_step):
if (i % 100 == 0):
print(i)
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
dist = self.measure.get_dist(self.x1, self.x2diff)
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
if (dist2 > dist):
# if(i==10):
fail_counter += 1
ave_inc += dist2 - dist
if (verbose):
print("x1", x1)
print("old x2", self.x2diff)
print("new x2", x2)
# print "atomistic x1", self.topology.to_atomistic(x1).flatten()
# print "atomistic x2", self.topology.to_atomistic(self.x2diff)
# print "new atomistic x2", self.topology.to_atomistic(x2)
print("dist", dist)
print("dist2", dist2)
print("i", i)
# try:
# import pele.utils.pymolwrapper as pym
# pym.start()
#
# x1 = self.topology.to_atomistic(x1)
# x2 = self.topology.to_atomistic(x2)
# self.x2diff = self.topology.to_atomistic(self.x2diff)
#
# pym.draw_rigid(x1, "A", 0.1, (1,0,0), self.system.draw_bonds)
# pym.draw_rigid(self.x2diff, "B", 0.1, (0,1,0), self.system.draw_bonds)
# pym.draw_rigid(x2, "C", 0.1, (0,0,1), self.system.draw_bonds)
# pym.draw_box(self.boxl, "D", 0.1)
#
# # pym.draw_rigid(x1[:self.nrigid*3], "A", 0.1, (1,0,0))
# # pym.draw_rigid(self.x2diff[:self.nrigid*3], "B", 0.1, (0,1,0))
# # pym.draw_rigid(x2[:self.nrigid*3], "C", 0.1, (0,0,1))
# # pym.draw_box(self.boxl, "D", 0.1)
#
# except:
# print "Could not draw using pymol, skipping this step"
else:
ave += dist - dist2
ave = ave / max_step
if (fail_counter > 0): ave_inc = ave_inc / fail_counter
print("average decrease in distance", ave)
print("average increase in distance", ave_inc)
self.assertFalse(fail_counter,
"alignment failed %d times" % fail_counter)
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)
class TestExactMatchPeriodic(unittest.TestCase):
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 randomly_permute(self, x):
import random
x = x.reshape(-1,3)
xnew = x.copy()
for atomlist in self.permlist:
permutation = copy.copy(atomlist)
random.shuffle(permutation)
xnew[atomlist,:] = x[permutation,:]
return xnew.flatten()
def test_exact_match(self):
self.assertTrue(self.exact_match(self.x1, self.x2trans))
def test_no_exact_match(self):
self.assertFalse(self.exact_match(self.x1, self.x2diff))
def test_exact_match_periodic(self):
self.x2same[:3] += self.boxl
self.assertTrue(self.exact_match(self.x1, self.x2same))
# This test is pretty superfluous for the atomic-system case. But it doesn't take long and probably
# doesn't hurt.
def test_align_translate(self):
np.random.seed(4)
n = self.nrigid
fail_counter = 0
for i in range(10000):
# if (i%100 == 0):
# print i
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
try:
dist, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
pass
if self.exact_match(self.x2diff,x2) is False:
fail_counter += 1
self.assertFalse(fail_counter, "bond lengths were changed %d times" % fail_counter)
def test_align_match(self):
np.random.seed(2)
fail_counter = 0
for i in range(1):
# if (i%100 == 0):
# print i
self.x1 = self.system.get_random_configuration()
self.x2trans = self.x1
translate = np.random.random(3)*self.boxl
self.transform.translate(self.x2trans, translate)
try:
dist, x1, x2 = self.mindist(self.x1, self.x2trans)
except RuntimeError:
pass
if (dist>1e-5):
fail_counter+=1
print dist
self.assertFalse(fail_counter, "structure matching failed %d times" % fail_counter)
def test_align_permutation(self):
np.random.seed(4)
fail_counter = 0
for i in range(1):
if (i%100 == 0):
print i
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
try:
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
except RuntimeError:
fail_counter+=1
self.assertFalse(fail_counter, "rotational alignment failed %d times" % fail_counter)
def test_align_improvement(self, verbose = True):
np.random.seed(6)
max_step = 10000
fail_counter = 0
ave = 0
ave_inc = 0
for i in range(max_step):
if (i%100 == 0):
print i
self.x1 = self.system.get_random_configuration()
self.x2diff = self.system.get_random_configuration()
dist = self.measure.get_dist(self.x1, self.x2diff)
dist2, x1, x2 = self.mindist(self.x1, self.x2diff)
if(dist2 > dist):
# if(i==10):
fail_counter += 1
ave_inc += dist2 - dist
if(verbose):
print "x1", x1
print "old x2", self.x2diff
print "new x2", x2
# print "atomistic x1", self.topology.to_atomistic(x1).flatten()
# print "atomistic x2", self.topology.to_atomistic(self.x2diff)
# print "new atomistic x2", self.topology.to_atomistic(x2)
print "dist", dist
print "dist2", dist2
print "i", i
# try:
# import pele.utils.pymolwrapper as pym
# pym.start()
#
# x1 = self.topology.to_atomistic(x1)
# x2 = self.topology.to_atomistic(x2)
# self.x2diff = self.topology.to_atomistic(self.x2diff)
#
# pym.draw_rigid(x1, "A", 0.1, (1,0,0), self.system.draw_bonds)
# pym.draw_rigid(self.x2diff, "B", 0.1, (0,1,0), self.system.draw_bonds)
# pym.draw_rigid(x2, "C", 0.1, (0,0,1), self.system.draw_bonds)
# pym.draw_box(self.boxl, "D", 0.1)
#
# # pym.draw_rigid(x1[:self.nrigid*3], "A", 0.1, (1,0,0))
# # pym.draw_rigid(self.x2diff[:self.nrigid*3], "B", 0.1, (0,1,0))
# # pym.draw_rigid(x2[:self.nrigid*3], "C", 0.1, (0,0,1))
# # pym.draw_box(self.boxl, "D", 0.1)
#
# except:
# print "Could not draw using pymol, skipping this step"
else:
ave += dist - dist2
ave = ave/max_step
if (fail_counter>0): ave_inc = ave_inc / fail_counter
print "average decrease in distance", ave
print "average increase in distance", ave_inc
self.assertFalse(fail_counter, "alignment failed %d times" % fail_counter)
