def test_generateNCMCIntegrator(self):
print('Testing AlchemicalExternalLangevinIntegrator')
cfg = {
'nstepsNC': 100,
'temperature': 100 * unit.kelvin,
'dt': 0.001 * unit.picoseconds,
'nprop': 2,
'propLambda': 0.1,
'splitting': 'V H R O R H V',
'alchemical_functions': {
'lambda_sterics': '1',
'lambda_electrostatics': '1'
}
}
ncmc_integrator = SimulationFactory.generateNCMCIntegrator(**cfg)
#Check we made the right integrator
assert isinstance(ncmc_integrator, AlchemicalExternalLangevinIntegrator)
#Check that the integrator has taken our Parameters
assert round(abs(ncmc_integrator.getTemperature()._value - cfg['temperature']._value), 7) == 0
assert ncmc_integrator.getStepSize() == cfg['dt']
assert ncmc_integrator._n_steps_neq == cfg['nstepsNC']
assert ncmc_integrator._n_lambda_steps == \
cfg['nstepsNC'] * cfg['nprop']
assert ncmc_integrator._alchemical_functions == \
cfg['alchemical_functions']
assert ncmc_integrator._splitting == cfg['splitting']
prop_range = (0.5 - cfg['propLambda'], 0.5 + cfg['propLambda'])
assert ncmc_integrator._prop_lambda == prop_range
def test_generateNCMCIntegrator(self):
print('Testing AlchemicalExternalLangevinIntegrator')
cfg = {
'nstepsNC': 100,
'temperature': 100 * unit.kelvin,
'dt': 0.001 * unit.picoseconds,
'nprop': 2,
'propLambda': 0.1,
'splitting': 'V H R O R H V',
'alchemical_functions': {
'lambda_sterics': '1',
'lambda_electrostatics': '1'
}
}
ncmc_integrator = SimulationFactory.generateNCMCIntegrator(**cfg)
#Check we made the right integrator
self.assertIsInstance(ncmc_integrator,
AlchemicalExternalLangevinIntegrator)
#Check that the integrator has taken our Parameters
self.assertAlmostEqual(ncmc_integrator.getTemperature()._value,
cfg['temperature']._value)
self.assertEqual(ncmc_integrator.getStepSize(), cfg['dt'])
self.assertEqual(ncmc_integrator._n_steps_neq, cfg['nstepsNC'])
self.assertEqual(ncmc_integrator._n_lambda_steps,
cfg['nstepsNC'] * cfg['nprop'])
self.assertEqual(ncmc_integrator._alchemical_functions,
cfg['alchemical_functions'])
self.assertEqual(ncmc_integrator._splitting, cfg['splitting'])
prop_range = (0.5 - cfg['propLambda'], 0.5 + cfg['propLambda'])
self.assertEqual(ncmc_integrator._prop_lambda, prop_range)
def ncmc_integrator(structure, system):
cfg = {
'nstepsNC': 10,
'temperature': 100 * unit.kelvin,
'dt': 0.001 * unit.picoseconds,
'nprop': 1,
'propLambda': 0.3,
'splitting': 'V H R O R H V',
'alchemical_functions': {
'lambda_sterics': '1',
'lambda_electrostatics': '1'
}
}
ncmc_integrator = SimulationFactory.generateNCMCIntegrator(**cfg)
return ncmc_integrator
def ncmc_integrator(structure, system):
cfg = {
'nstepsNC': 10,
'temperature': 100 * unit.kelvin,
'dt': 0.001 * unit.picoseconds,
'nprop': 1,
'propLambda': 0.3,
'splitting': 'V H R O R H V',
'alchemical_functions': {
'lambda_sterics': '1',
'lambda_electrostatics': '1'
}
}
ncmc_integrator = SimulationFactory.generateNCMCIntegrator(**cfg)
return ncmc_integrator
