mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
e53bdc5eab
* Top level Python module is now "openmm" * Updated module names in examples * Updated module names in documentation * Updated module in CI scripts * Added deprecation warning
86 lines
3.7 KiB
Python
86 lines
3.7 KiB
Python
import unittest
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import math
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from openmm import Vec3
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from openmm.unit import *
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from openmm.app.internal.unitcell import computePeriodicBoxVectors
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from openmm.app.internal.unitcell import computeLengthsAndAngles
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from openmm.app.internal.unitcell import reducePeriodicBoxVectors
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def strip_units(x):
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if is_quantity(x): return x.value_in_unit_system(md_unit_system)
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return x
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class TestUnitCell(unittest.TestCase):
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""" Test the unitcell.py module """
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def testReducePBCVectors(self):
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""" Checks that reducePeriodicBoxVectors properly reduces vectors """
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a = Vec3(4.24388485, 0.0, 0.0)
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b = Vec3(-1.4146281691908937, 4.001173048368583, 0.0)
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c = Vec3(-1.4146281691908937, -2.0005862820516203, 3.4651176446201674)
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vecs = reducePeriodicBoxVectors((a, b, c)*nanometers)
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vecs2 = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
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109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
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# Check that the vectors are the same
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a1, a2, a3 = vecs
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b1, b2, b3 = vecs2
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for x, y in zip(a1, b1):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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for x, y in zip(a2, b2):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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for x, y in zip(a3, b3):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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def testComputePBCVectors(self):
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""" Tests computing periodic box vectors """
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deg90 = 90 * degrees
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vecs = computePeriodicBoxVectors(1, 2, 3, deg90, deg90, deg90)
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a, b, c = vecs
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self.assertAlmostEqual(a[0]/nanometers, 1)
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self.assertAlmostEqual(a[1]/nanometers, 0)
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self.assertAlmostEqual(a[2]/nanometers, 0)
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self.assertAlmostEqual(b[0]/nanometers, 0)
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self.assertAlmostEqual(b[1]/nanometers, 2)
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self.assertAlmostEqual(b[2]/nanometers, 0)
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self.assertAlmostEqual(c[0]/nanometers, 0)
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self.assertAlmostEqual(c[1]/nanometers, 0)
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self.assertAlmostEqual(c[2]/nanometers, 3)
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# Make sure round-trip works
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la, lb, lc, al, be, ga = computeLengthsAndAngles(vecs)
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self.assertAlmostEqual(la, 1)
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self.assertAlmostEqual(lb, 2)
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self.assertAlmostEqual(lc, 3)
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self.assertAlmostEqual(al, math.pi / 2)
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self.assertAlmostEqual(be, math.pi / 2)
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self.assertAlmostEqual(ga, math.pi / 2)
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# Now test a truncated octahedron. Can't do a simple round-trip though,
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# due to the reduced form. So test the *second* round-trip, which should
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# yield the same measurements
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vecs = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
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109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
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la, lb, lc, al, be, ga = computeLengthsAndAngles(vecs)
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vecs2 = computePeriodicBoxVectors(la, lb, lc, al, be, ga)
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la2, lb2, lc2, al2, be2, ga2 = computeLengthsAndAngles(vecs2)
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# Now make sure that the round-trip worked
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self.assertAlmostEqual(strip_units(la), strip_units(la2))
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self.assertAlmostEqual(strip_units(lb), strip_units(lb2))
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self.assertAlmostEqual(strip_units(lc), strip_units(lc2))
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self.assertAlmostEqual(strip_units(al), strip_units(al2))
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self.assertAlmostEqual(strip_units(be), strip_units(be2))
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self.assertAlmostEqual(strip_units(ga), strip_units(ga2))
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# Check that the vectors are the same
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a1, a2, a3 = vecs
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b1, b2, b3 = vecs2
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for x, y in zip(a1, b1):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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for x, y in zip(a2, b2):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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for x, y in zip(a3, b3):
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self.assertAlmostEqual(strip_units(x), strip_units(y))
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