def setUp(self):
a = Vector(1.5, 0.3, 0.)
b = Vector(-0.1, 0.8, 0.2)
c = Vector(0., -0.2, 1.1)
self.universe = ParallelepipedicPeriodicUniverse((a, b, c))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position=p))
def setUp(self):
a = Vector(1.5, 0.3, 0.)
b = Vector(-0.1, 0.8, 0.2)
c = Vector(0., -0.2, 1.1)
self.universe = ParallelepipedicPeriodicUniverse((a, b, c))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position = p))
def test_boxCoordinates1(self):
for i in range(500):
p = randomPointInBox(5.)
pt = self.universe.realToBoxCoordinates(p)
self.assert_(
(self.universe.boxToRealCoordinates(pt) - p).length() < 1.e-14)
pt = self.universe.boxToRealCoordinates(p)
self.assert_(
(self.universe.realToBoxCoordinates(pt) - p).length() < 1.e-14)
def test_boxCoordinates1(self):
for i in range(500):
p = randomPointInBox(5.)
pt = self.universe.realToBoxCoordinates(p)
self.assert_((self.universe.boxToRealCoordinates(pt)-p).length()
< 1.e-14)
pt = self.universe.boxToRealCoordinates(p)
self.assert_((self.universe.realToBoxCoordinates(pt)-p).length()
< 1.e-14)
def test_coordinateFold(self):
for i in range(500):
self.universe.translateBy(randomPointInBox(0.5))
self.universe.foldCoordinatesIntoBox()
for atom in self.universe.atomList():
rb = self.universe.realToBoxCoordinates(atom.position())
self.assert_(rb[0] >= -0.5)
self.assert_(rb[1] >= -0.5)
self.assert_(rb[2] >= -0.5)
self.assert_(rb[0] <= 0.5)
self.assert_(rb[1] <= 0.5)
self.assert_(rb[2] <= 0.5)
cconf = self.universe.contiguousObjectConfiguration(
self.universe.objectList())
for o in self.universe:
for bu in o.bondedUnits():
for bond in bu.bonds:
l = (bond.a1.position(cconf) -
bond.a2.position(cconf)).length()
self.assert_(l < 0.16)
def test_coordinateFold(self):
for i in range(500):
self.universe.translateBy(randomPointInBox(0.5))
self.universe.foldCoordinatesIntoBox()
for atom in self.universe.atomList():
rb = self.universe.realToBoxCoordinates(atom.position())
self.assert_(rb[0] >= -0.5)
self.assert_(rb[1] >= -0.5)
self.assert_(rb[2] >= -0.5)
self.assert_(rb[0] <= 0.5)
self.assert_(rb[1] <= 0.5)
self.assert_(rb[2] <= 0.5)
cconf = self.universe.contiguousObjectConfiguration(
self.universe.objectList())
for o in self.universe:
for bu in o.bondedUnits():
for bond in bu.bonds:
l = (bond.a1.position(cconf)
- bond.a2.position(cconf)).length()
self.assert_(l < 0.16)
# Calculate the size of the box
density = 1.*Units.g/(Units.cm)**3
number_density = density/Molecule('water').mass()
real_size = (n_molecules/number_density)**(1./3.)
# Create the universe with a larger initial size
current_size = 5.*real_size
world = CubicPeriodicUniverse(current_size,
Amber94ForceField(1.2*Units.nm,
{'method': 'ewald'}))
# Add solvent molecules at random positions, avoiding the neighbourhood
# of previously placed molecules
excluded_regions = []
for i in range(n_molecules):
m = Molecule('water', position = randomPointInBox(current_size))
while 1:
s = m.boundingSphere()
collision = 0
for region in excluded_regions:
if s.intersectWith(region) is not None:
collision = 1
break
if not collision:
break
m.translateTo(randomPointInBox(current_size))
world.addObject(m)
excluded_regions.append(s)
# Reduce energy
minimizer = SteepestDescentMinimizer(world, step_size = 0.05*Units.Ang)
def setUp(self):
self.universe = OrthorhombicPeriodicUniverse((1.5, 0.8, 1.1))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position = p))
def setUp(self):
self.universe = InfiniteUniverse()
for i in range(100):
p = randomPointInBox(1.)
self.universe.addObject(Atom('C', position = p))
# Calculate the size of the box
density = 1. * Units.g / (Units.cm)**3
number_density = density / Molecule('water').mass()
real_size = (n_molecules / number_density)**(1. / 3.)
# Create the universe with a larger initial size
current_size = 5. * real_size
world = CubicPeriodicUniverse(
current_size, Amber94ForceField(1.2 * Units.nm, {'method': 'ewald'}))
# Add solvent molecules at random positions, avoiding the neighbourhood
# of previously placed molecules
excluded_regions = []
for i in range(n_molecules):
m = Molecule('water', position=randomPointInBox(current_size))
while 1:
s = m.boundingSphere()
collision = 0
for region in excluded_regions:
if s.intersectWith(region) is not None:
collision = 1
break
if not collision:
break
m.translateTo(randomPointInBox(current_size))
world.addObject(m)
excluded_regions.append(s)
# Reduce energy
minimizer = SteepestDescentMinimizer(world, step_size=0.05 * Units.Ang)
def setUp(self):
self.universe = OrthorhombicPeriodicUniverse((1.5, 0.8, 1.1))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position=p))
def setUp(self):
self.universe = InfiniteUniverse()
for i in range(100):
p = randomPointInBox(1.)
self.universe.addObject(Atom('C', position=p))