def test_vvvr_shadow_work_accumulation():
"""When `measure_shadow_work==True`, assert that global `shadow_work` is initialized to zero and
reaches a nonzero value after integrating a few dozen steps."""
# test `measure_shadow_work=True` --> accumulation of a nonzero value in global `shadow_work`
testsystem = testsystems.HarmonicOscillator()
system, topology = testsystem.system, testsystem.topology
temperature = 298.0 * unit.kelvin
integrator = integrators.VVVRIntegrator(temperature, measure_shadow_work=True)
context = openmm.Context(system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(temperature)
assert(integrator.get_shadow_work(dimensionless=True) == 0), "Shadow work should initially be zero."
assert(integrator.get_shadow_work() / unit.kilojoules_per_mole == 0), "integrator.get_shadow_work() should have units of energy."
assert(integrator.shadow_work / unit.kilojoules_per_mole == 0), "integrator.shadow_work should have units of energy."
integrator.step(25)
assert(integrator.get_shadow_work(dimensionless=True) != 0), "integrator.get_shadow_work() should be nonzero after dynamics"
integrator = integrators.VVVRIntegrator(temperature)
context = openmm.Context(system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(25)
del context, integrator
def test_external_protocol_work_accumulation():
"""When `measure_protocol_work==True`, assert that global `protocol_work` is initialized to zero and
reaches a zero value after integrating a few dozen steps without perturbation.
By default (`measure_protocol_work=False`), assert that there is no global name for `protocol_work`."""
testsystem = testsystems.HarmonicOscillator()
system, topology = testsystem.system, testsystem.topology
temperature = 298.0 * unit.kelvin
integrator = integrators.ExternalPerturbationLangevinIntegrator(splitting="O V R V O", temperature=temperature)
context = openmm.Context(system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(temperature)
# Check that initial step accumulates no protocol work
assert(integrator.get_protocol_work(dimensionless=True) == 0), "Protocol work should be 0 initially"
assert(integrator.get_protocol_work() / unit.kilojoules_per_mole == 0), "Protocol work should have units of energy"
integrator.step(1)
assert(integrator.get_protocol_work(dimensionless=True) == 0), "There should be no protocol work."
# Check that a single step accumulates protocol work
pe_1 = context.getState(getEnergy=True).getPotentialEnergy()
perturbed_K=99.0 * unit.kilocalories_per_mole / unit.angstroms**2
context.setParameter('testsystems_HarmonicOscillator_K', perturbed_K)
pe_2 = context.getState(getEnergy=True).getPotentialEnergy()
integrator.step(1)
assert (integrator.get_protocol_work(dimensionless=True) != 0), "There should be protocol work after perturbing."
assert (integrator.protocol_work == (pe_2 - pe_1)), "The potential energy difference should be equal to protocol work."
del context, integrator
integrator = integrators.VVVRIntegrator(temperature)
context = openmm.Context(system, integrator)
context.setPositions(testsystem.positions)
context.setVelocitiesToTemperature(temperature)
integrator.step(25)
del context, integrator
for replicate in range(nreplicates):
# Reconstitute System object.
print "Reconstituting System object..."
system = openmm.System()
system.__setstate__(str(ncfile.variables['system'][0]))
# Add a barostat to the system.
# NOTE: This is added to a new copy of the system to ensure barostat random number seeds are unique.
print "Adding barostat..."
barostat = openmm.MonteCarloBarostat(pressure, temperature,
barostat_frequency)
system.addForce(barostat)
# Create integrator
print "Creating integrator..."
integrator = integrators.VVVRIntegrator(temperature, collision_rate,
timestep)
# Create context.
print "Creating Context..."
context = openmm.Context(system, integrator)
# Set initial conditions.
print "Setting initial positions..."
context.setPositions(initial_positions)
print "Setting initial velocities appropriate for temperature..."
context.setVelocitiesToTemperature(temperature)
# Allocate storage for data
reduced_density_t = np.zeros([niterations + 1], np.float32)
reduced_potential_t = np.zeros([niterations + 1], np.float32)