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Merge pull request #1484 from pkreissl/test_interaction_potentials
Test interaction potentials
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| # | ||
| # Copyright (C) 2013,2014,2015,2016 The ESPResSo project | ||
| # | ||
| # This file is part of ESPResSo. | ||
| # | ||
| # ESPResSo is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # ESPResSo is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| # | ||
| from __future__ import print_function | ||
| import espressomd | ||
| import numpy | ||
| import unittest as ut | ||
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| class InteractionsNonBondedTest(ut.TestCase): | ||
| system = espressomd.System() | ||
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| box_l = 10. | ||
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| start_pos = numpy.random.rand(3) * box_l | ||
| axis = numpy.random.rand(3) | ||
| axis /= numpy.linalg.norm(axis) | ||
| rel_pos = numpy.cross(numpy.random.rand(3), axis) | ||
| rel_pos /= numpy.linalg.norm(rel_pos) | ||
|
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| def setUp(self): | ||
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| self.system.box_l = [self.box_l] * 3 | ||
| self.system.cell_system.skin = 0.4 | ||
| self.system.time_step = 1. | ||
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| self.system.part.add(id=0, pos=self.start_pos, type=0) | ||
| self.system.part.add(id=1, pos=self.start_pos + self.rel_pos, type=0) | ||
| self.system.part.add(id=2, pos=self.start_pos + self.rel_pos, type=0) | ||
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| def tearDown(self): | ||
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| self.system.part.clear() | ||
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| def rotate_vector(self, v, k, phi): | ||
| """Rotates vector v around unit vector k by angle phi. | ||
| Uses Rodrigues' rotation formula.""" | ||
| vrot = v * numpy.cos(phi) + numpy.cross(k, v) * \ | ||
| numpy.sin(phi) + k * numpy.dot(k, v) * (1 - numpy.cos(phi)) | ||
| return vrot | ||
|
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| # Required, since assertAlmostEqual does NOT check significant places | ||
| def assertFractionAlmostEqual(self, a, b, places=10): | ||
| if abs(b) < 1E-8: | ||
| self.assertAlmostEqual(a, b) | ||
| else: | ||
| self.assertAlmostEqual(a / b, 1., places=4) | ||
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| def assertItemsFractionAlmostEqual(self, a, b): | ||
| for i, ai in enumerate(a): | ||
| self.assertFractionAlmostEqual(ai, b[i]) | ||
|
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| # Analytical Expression | ||
| def angle_harmonic_potential(self, phi, bend=1.0, phi0=numpy.pi): | ||
| return 0.5 * bend * numpy.power(phi - phi0, 2) | ||
|
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| # Test Angle Harmonic Potential | ||
| @ut.skipIf(not espressomd.has_features(["BOND_ANGLE"]), | ||
| "Features not available, skipping test!") | ||
| def test_angle_harmonic(self): | ||
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| ah_bend = 1. | ||
| ah_phi0 = 0.4327 * numpy.pi | ||
|
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| angle_harmonic = espressomd.interactions.Angle_Harmonic( | ||
| bend=ah_bend, phi0=ah_phi0) | ||
| self.system.bonded_inter.add(angle_harmonic) | ||
| self.system.part[0].add_bond((angle_harmonic, 1, 2)) | ||
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| N = 111 | ||
| d_phi = numpy.pi / N | ||
| for i in range(N): | ||
| self.system.part[2].pos = self.start_pos + \ | ||
| self.rotate_vector(self.rel_pos, self.axis, i * d_phi) | ||
| self.system.integrator.run(recalc_forces=True, steps=0) | ||
|
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| # Calculate energies | ||
| E_sim = self.system.analysis.energy()["bonded"] | ||
| E_ref = self.angle_harmonic_potential( | ||
| phi=i * d_phi, bend=ah_bend, phi0=ah_phi0) | ||
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| # Check that energies match | ||
| self.assertFractionAlmostEqual(E_sim, E_ref) | ||
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| if __name__ == '__main__': | ||
| print("Features: ", espressomd.features()) | ||
| ut.main() |
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