mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
e62bdf6adb
* Can use getPlatform() instead of getPlatformByName() * More concise arguments for getState()
123 lines
5.0 KiB
Python
123 lines
5.0 KiB
Python
import unittest
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from openmm import app
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import openmm as mm
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from openmm import unit
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try:
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import numpy as np
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NUMPY_IMPORT_FAILED = False
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except ImportError:
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NUMPY_IMPORT_FAILED = True
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@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
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class TestNumpyCompatibility(unittest.TestCase):
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def setUp(self):
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prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
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system = prmtop.createSystem(nonbondedMethod=app.PME,
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nonbondedCutoff=0.9*unit.nanometers,
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constraints=app.HBonds, rigidWater=True,
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ewaldErrorTolerance=0.0005)
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integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds,
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2.0*unit.femtoseconds)
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self.simulation = app.Simulation(prmtop.topology, system, integrator,
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mm.Platform.getPlatform('Reference'))
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def test_setPositions(self):
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n_particles = self.simulation.context.getSystem().getNumParticles()
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input = np.random.randn(n_particles, 3)
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self.simulation.context.setPositions(input)
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output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
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np.testing.assert_array_almost_equal(input, output)
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def test_setPositions_units(self):
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n_particles = self.simulation.context.getSystem().getNumParticles()
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input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms)
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self.simulation.context.setPositions(input)
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output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
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np.testing.assert_array_almost_equal(input.value_in_unit(unit.nanometers), output.value_in_unit(unit.nanometers))
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def test_setVelocities(self):
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n_particles = self.simulation.context.getSystem().getNumParticles()
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input = np.random.randn(n_particles, 3)
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self.simulation.context.setVelocities(input)
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output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
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np.testing.assert_array_almost_equal(input, output)
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def test_setVelocities_units(self):
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n_particles = self.simulation.context.getSystem().getNumParticles()
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input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms / unit.femtoseconds)
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self.simulation.context.setVelocities(input)
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output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
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np.testing.assert_array_almost_equal(input.value_in_unit(unit.angstroms / unit.femtoseconds),
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output.value_in_unit(unit.angstroms / unit.femtoseconds))
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def test_periodicBoxVectors(self):
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output = self.simulation.context.getState(getVelocities=True).getPeriodicBoxVectors(asNumpy=True)
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systemBox = self.simulation.system.getDefaultPeriodicBoxVectors()
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for i in range(3):
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np.testing.assert_array_almost_equal(systemBox[i].value_in_unit(unit.nanometers), output[i].value_in_unit(unit.nanometers))
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def test_tabulatedFunction(self):
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f = mm.CustomNonbondedForce('g(r)')
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r = np.linspace(0,10)
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g_of_r = np.sin(r)
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indx = f.addFunction('g', g_of_r, np.min(r), np.max(r))
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name, g_of_r_out, min_r_out, max_r_out = f.getFunctionParameters(indx)
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np.testing.assert_array_almost_equal(g_of_r, np.asarray(g_of_r_out))
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assert min_r_out == np.min(r)
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assert max_r_out == np.max(r)
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def test_CMAP(self):
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f = mm.CMAPTorsionForce()
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energy = np.random.randn(10*10)
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f.addMap(10, energy)
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size, energy_out = f.getMapParameters(0)
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energy_out = energy_out.value_in_unit_system(unit.md_unit_system)
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self.assertEqual(size, 10)
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np.testing.assert_array_almost_equal(energy, np.asarray(energy_out))
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def test_int64(self):
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indices = np.array([0,1,2])
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sys = mm.System()
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sys.addParticle(2.0)
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assert sys.getParticleMass(indices[0]) == 2.0*unit.amu
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@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
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class TestNumpyUnits(unittest.TestCase):
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def setUp(self):
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self.data = unit.Quantity(np.arange(300), unit.nanometers)
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def testNumpyAttributes(self):
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d = self.data.reshape((100, 3))
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self.assertTrue(unit.is_quantity(d) and d.unit is unit.nanometers)
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self.assertTrue(unit.is_quantity(d.sum()))
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self.assertTrue(unit.is_quantity(d.sum(axis=0)))
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self.assertTrue(unit.is_quantity(d.std()))
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self.assertTrue(unit.is_quantity(d.std(axis=0)))
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self.assertTrue(unit.is_quantity(d.max()))
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self.assertTrue(unit.is_quantity(d.max(axis=1)))
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self.assertTrue(unit.is_quantity(d.min()))
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self.assertTrue(unit.is_quantity(d.min(axis=0)))
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self.assertTrue(unit.is_quantity(d.mean()))
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self.assertTrue(unit.is_quantity(d.mean(axis=1)))
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if __name__ == '__main__':
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unittest.main()
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