def _construct_box_vectors(line):
"""Create the periodic box vectors based on the values stored in the file.
@param[in] line The line containing the description
"""
sline = line.split()
values = [float(i) for i in sline]
if len(sline) == 3:
return (Vec3(values[0], 0, 0), Vec3(0, values[1], 0), Vec3(0, 0, values[2]))*nanometers
return reducePeriodicBoxVectors((Vec3(values[0], values[3], values[4]), Vec3(values[5], values[1], values[6]), Vec3(values[7], values[8], values[2]))*nanometers)
def _construct_box_vectors(line):
"""Create the periodic box vectors based on the values stored in the file.
@param[in] line The line containing the description
"""
sline = line.split()
values = [float(i) for i in sline]
if len(sline) == 3:
return (Vec3(values[0], 0, 0), Vec3(
0, values[1], 0), Vec3(0, 0, values[2])) * nanometers
return reducePeriodicBoxVectors(
(Vec3(values[0], values[3],
values[4]), Vec3(values[5], values[1], values[6]),
Vec3(values[7], values[8], values[2])) * nanometers)
def testReducePBCVectors(self):
""" Checks that reducePeriodicBoxVectors properly reduces vectors """
a = Vec3(4.24388485, 0.0, 0.0)
b = Vec3(-1.4146281691908937, 4.001173048368583, 0.0)
c = Vec3(-1.4146281691908937, -2.0005862820516203, 3.4651176446201674)
vecs = reducePeriodicBoxVectors((a, b, c)*nanometers)
vecs2 = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
# Check that the vectors are the same
a1, a2, a3 = vecs
b1, b2, b3 = vecs2
for x, y in zip(a1, b1):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a2, b2):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a3, b3):
self.assertAlmostEqual(strip_units(x), strip_units(y))
def reduced_box_vectors(snapshot):
"""Reduced box vectors for a snapshot (with units)
See also
--------
reduce_trajectory_box_vectors
Parameters
----------
snapshot : :class:`.Snapshot`
input snapshot
Returns
-------
:class:`.Snapshot`
snapshot with correctly reduced box vectors
"""
nm = unit.nanometer
return np.array(
reducePeriodicBoxVectors(snapshot.box_vectors).value_in_unit(nm)) * nm
def testReducePBCVectors(self):
""" Checks that reducePeriodicBoxVectors properly reduces vectors """
a = Vec3(4.24388485, 0.0, 0.0)
b = Vec3(-1.4146281691908937, 4.001173048368583, 0.0)
c = Vec3(-1.4146281691908937, -2.0005862820516203, 3.4651176446201674)
vecs = reducePeriodicBoxVectors((a, b, c) * nanometers)
vecs2 = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
109.4712190 * degrees,
109.4712190 * degrees,
109.4712190 * degrees)
# Check that the vectors are the same
a1, a2, a3 = vecs
b1, b2, b3 = vecs2
for x, y in zip(a1, b1):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a2, b2):
self.assertAlmostEqual(strip_units(x), strip_units(y))
for x, y in zip(a3, b3):
self.assertAlmostEqual(strip_units(x), strip_units(y))
def reduced_box_vectors(snapshot):
"""Reduced box vectors for a snapshot (with units)
See also
--------
reduce_trajectory_box_vectors
Parameters
----------
snapshot : :class:`.Snapshot`
input snapshot
Returns
-------
:class:`.Snapshot`
snapshot with correctly reduced box vectors
"""
nm = u.nanometer
return np.array(
reducePeriodicBoxVectors(snapshot.box_vectors).value_in_unit(nm)
) * nm
