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# Restraint tests
#
# Written by Konrad Hinsen
#
import unittest
from subsets import SubsetTest
from MMTK import *
from MMTK.ForceFields import Restraints, SPCEForceField
from Scientific import N
class TrapTest(unittest.TestCase):
def setUp(self):
self.universe1 = InfiniteUniverse()
atom = Atom('C', position=Vector(0.5, 0., 0.))
self.universe1.addObject(atom)
ff = Restraints.HarmonicTrapForceField(atom,
Vector(-0.5, 0., 0.),
1.)
self.universe1.setForceField(ff)
self.universe2 = InfiniteUniverse()
atom1 = Atom('C', position=Vector(0.25, 0., 0.))
atom2 = Atom('C', position=Vector(0.75, 0., 0.))
cluster = Collection([atom1, atom2])
self.universe2.addObject(cluster)
ff = Restraints.HarmonicTrapForceField(cluster,
Vector(-0.5, 0., 0.),
1.)
self.universe2.setForceField(ff)
self.universe3 = InfiniteUniverse()
water = Molecule('water', position=Vector(0.5, 0., 0.))
self.universe3.addObject(water)
ff = Restraints.HarmonicTrapForceField(water,
Vector(-0.5, 0., 0.),
1.)
self.universe3.setForceField(ff)
def test_energy_one_atom(self):
e, g, fc = self.universe1.energyGradientsAndForceConstants()
self.assertAlmostEqual(e, 1., 7)
self.assert_((g[0]-Vector(2., 0., 0.)).length() < 1.e-5)
fc = fc[0, 0]
for i in range(3):
for j in range(3):
if i == j:
self.assertAlmostEqual(fc[i, j], 2., 7)
else:
self.assertAlmostEqual(fc[i,j], 0., 7)
def test_energy_two_atoms(self):
e, g, fc = self.universe2.energyGradientsAndForceConstants()
self.assertAlmostEqual(e, 1., 7)
self.assert_((g[0]-Vector(1., 0., 0.)).length() < 1.e-5)
self.assert_((g[1]-Vector(1., 0., 0.)).length() < 1.e-5)
for a1 in [0, 1]:
for a2 in [0, 1]:
fc12 = fc[a1, a2]
for i in range(3):
for j in range(3):
if i == j:
self.assertAlmostEqual(fc12[i, j], 0.5, 7)
else:
self.assertAlmostEqual(fc12[i,j], 0., 7)
def test_energy_water(self):
H1 = self.universe3[0].H1
H2 = self.universe3[0].H2
O = self.universe3[0].O
e, g, fc = self.universe3.energyGradientsAndForceConstants()
self.assertAlmostEqual(e, 1., 7)
self.assert_((g[H1]-g[H2]).length() < 1.e-5)
self.assert_((g[H1]-g[O]*H1.mass()/O.mass()).length() < 1.e-5)
m = 2*H1.mass() + O.mass()
for a1 in [H1, H2, O]:
for a2 in [H1, H2, O]:
fc12 = fc[a1, a2]
f = 2.*a1.mass()*a2.mass()/(m*m)
for i in range(3):
for j in range(3):
if i == j:
self.assertAlmostEqual(fc12[i, j], f, 7)
else:
self.assertAlmostEqual(fc12[i,j], 0., 7)
def test_subsets(self):
H1 = self.universe3[0].H1
H2 = self.universe3[0].H2
O = self.universe3[0].O
subset = Collection([H1, H2, O])
e = self.universe3.energy(subset)
self.assertAlmostEqual(e, 1., 7)
subset = Collection()
e = self.universe3.energy(subset)
self.assertAlmostEqual(e, 0., 7)
subset = Collection([H1, H2])
self.assertRaises(ValueError, self.universe3.energy, subset)
class DistanceTest(unittest.TestCase):
def setUp(self):
self.universe1 = InfiniteUniverse()
atom1 = Atom('C', position=Vector(0.5, 0., 0.))
atom2 = Atom('C', position=Vector(-0.5, 0., 0.))
self.universe1.addObject(atom1)
self.universe1.addObject(atom2)
ff = Restraints.HarmonicDistanceRestraint(atom1, atom2,
0.9, 1.)
self.universe1.setForceField(ff)
self.universe2 = InfiniteUniverse()
atom1 = Atom('C', position=Vector(0.25, 0., 0.))
atom2 = Atom('C', position=Vector(0.75, 0., 0.))
cluster1 = Collection([atom1, atom2])
atom3 = Atom('C', position=Vector(-0.75, 0., 0.))
atom4 = Atom('C', position=Vector(-0.25, 0., 0.))
cluster2 = Collection([atom3, atom4])
self.universe2.addObject(cluster1)
self.universe2.addObject(cluster2)
ff = Restraints.HarmonicDistanceRestraint(cluster1, cluster2,
0.9, 1.)
self.universe2.setForceField(ff)
self.universe3 = InfiniteUniverse()
water1 = Molecule('water', position=Vector(0.5, 0., 0.))
water2 = Molecule('water', position=Vector(-0.5, 0., 0.))
self.universe3.addObject(water1)
self.universe3.addObject(water2)
ff = Restraints.HarmonicDistanceRestraint(water1, water2,
0.9, 1.)
self.universe3.setForceField(ff)
def test_energy_single_atoms(self):
e, g, fc = self.universe1.energyGradientsAndForceConstants()
self.assertAlmostEqual(e, 0.01, 7)
self.assert_((g[0]-Vector(0.2, 0., 0.)).length() < 1.e-5)
fc = fc[0, 0]
fc_ref = [2., 0.2, 0.2]
for i in range(3):
self.assertAlmostEqual(fc[i, i], fc_ref[i], 7)
for j in range(3):
if i != j:
self.assertAlmostEqual(fc[i,j], 0., 7)
def test_energy_atom_pairs(self):
e, g, fc = self.universe2.energyGradientsAndForceConstants()
self.assertAlmostEqual(e, 0.01, 7)
self.assert_((g[0]-Vector(0.1, 0., 0.)).length() < 1.e-5)
self.assert_((g[1]-Vector(0.1, 0., 0.)).length() < 1.e-5)
self.assert_((g[2]-Vector(-0.1, 0., 0.)).length() < 1.e-5)
self.assert_((g[3]-Vector(-0.1, 0., 0.)).length() < 1.e-5)
p1 = [0, 1]
p2 = [2, 3]
fc_ref = [0.5, 0.05, 0.05]
for a1 in range(4):
for a2 in range(4):
fcp = fc[a1, a2]
for i in range(3):
if (a1 in p1 and a2 in p1) or (a1 in p2 and a2 in p2):
self.assertAlmostEqual(fcp[i, i], fc_ref[i], 7)
else:
self.assertAlmostEqual(fcp[i, i], -fc_ref[i], 7)
for j in range(3):
if i != j:
self.assertAlmostEqual(fcp[i,j], 0., 7)
def test_energy_water(self):
e, g, fc = self.universe3.energyGradientsAndForceConstants()
fc_ref = [2., 0.2, 0.2]
self.assertAlmostEqual(e, 0.01, 7)
for m, s in [(self.universe3[0], 1), (self.universe3[1], -1),]:
self.assert_((g[m.H1]-g[m.H2]).length() < 1.e-5)
self.assert_((g[m.H1]-g[m.O]*m.H1.mass()/m.O.mass()).length()
< 1.e-5)
mass = 2*m.H1.mass() + m.O.mass()
for a1 in [m.H1, m.H2, m.O]:
for a2 in [m.H1, m.H2, m.O]:
fc12 = fc[a1, a2]
f = a1.mass()*a2.mass()/(mass*mass)
for i in range(3):
for j in range(3):
if i == j:
self.assertAlmostEqual(fc12[i, j], f*fc_ref[i], 7)
else:
self.assertAlmostEqual(fc12[i,j], 0., 7)
def test_subsets(self):
m1 = self.universe3[0]
m2 = self.universe3[1]
subset = Collection([m1.H1, m1.H2, m1.O, m2.H1, m2.H2, m2.O])
e = self.universe3.energy(subset)
self.assertAlmostEqual(e, 0.01, 7)
subset = Collection()
e = self.universe3.energy(subset)
self.assertAlmostEqual(e, 0., 7)
subset = Collection([m1.H1, m2.H2])
self.assertRaises(ValueError, self.universe3.energy, subset)
class NonbondedExclusionTest(unittest.TestCase):
def test_exclusion(self):
universe = InfiniteUniverse()
w1 = Molecule('water', position=(Vector(-0.2, 0., 0.)))
w2 = Molecule('water', position=(Vector(+0.2, 0., 0.)))
universe.addObject(w1)
universe.addObject(w2)
ff = SPCEForceField() + \
Restraints.HarmonicDistanceRestraint(w1.O, w2.O, 0.35, 1., False)
universe.setForceField(ff)
self.assert_(universe.energyTerms()['Lennard-Jones'] < -0.1)
ff = SPCEForceField() + \
Restraints.HarmonicDistanceRestraint(w1.O, w2.O, 0.35, 1., True)
universe.setForceField(ff)
self.assertAlmostEqual(universe.energyTerms()['Lennard-Jones'], 0., 7)
def suite():
loader = unittest.TestLoader()
s = unittest.TestSuite()
s.addTest(loader.loadTestsFromTestCase(TrapTest))
s.addTest(loader.loadTestsFromTestCase(DistanceTest))
s.addTest(loader.loadTestsFromTestCase(NonbondedExclusionTest))
return s
if __name__ == '__main__':
unittest.main()
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