def test_pressure_with_exceptions():
system, positions, topology = readSystem('emim_BCN4_Jiung2014')
platform = openmm.Platform.getPlatformByName('Reference')
computer = atomsmm.PressureComputer(system,
topology,
platform,
temperature=300 * unit.kelvin)
context = openmm.Context(system, openmm.CustomIntegrator(0), platform)
context.setPositions(positions)
state = context.getState(getPositions=True,
getVelocities=True,
getForces=True)
computer.import_configuration(state)
atomic_virial = computer.get_atomic_virial()
assert atomic_virial / atomic_virial.unit == pytest.approx(
-22827.477810819175)
atomic_pressure = computer.get_atomic_pressure()
assert atomic_pressure / atomic_pressure.unit == pytest.approx(
-282.7243180164338)
molecular_virial = computer.get_molecular_virial(state.getForces())
assert molecular_virial / molecular_virial.unit == pytest.approx(
-23272.958585794207)
molecular_pressure = computer.get_molecular_pressure(state.getForces())
assert molecular_pressure / molecular_pressure.unit == pytest.approx(
-3283.563262288828)
def test_pressure_with_bath_temperature():
system, positions, topology = readSystem('q-SPC-FW')
platform = openmm.Platform.getPlatformByName('Reference')
computer = atomsmm.PressureComputer(system,
topology,
platform,
temperature=300 * unit.kelvin)
context = openmm.Context(system, openmm.CustomIntegrator(0), platform)
context.setPositions(positions)
state = context.getState(getPositions=True,
getVelocities=True,
getForces=True)
computer.import_configuration(state)
atomic_virial = computer.get_atomic_virial()
assert atomic_virial / atomic_virial.unit == pytest.approx(
-11661.677650154408)
atomic_pressure = computer.get_atomic_pressure()
assert atomic_pressure / atomic_pressure.unit == pytest.approx(
-58.64837784125407)
molecular_virial = computer.get_molecular_virial(state.getForces())
assert molecular_virial / molecular_virial.unit == pytest.approx(
-5418.629781093525)
molecular_pressure = computer.get_molecular_pressure(state.getForces())
assert molecular_pressure / molecular_pressure.unit == pytest.approx(
-554.9525554206972)
def test_pressure_with_kinetic_temperature():
system, positions, topology = readSystem('q-SPC-FW')
platform = openmm.Platform.getPlatformByName('Reference')
computer = atomsmm.PressureComputer(system, topology, platform)
context = openmm.Context(system, openmm.CustomIntegrator(0), platform)
context.setPositions(positions)
context.setVelocitiesToTemperature(300 * unit.kelvin, 1234)
state = context.getState(getPositions=True,
getVelocities=True,
getForces=True)
computer.import_configuration(state)
atomic_virial = computer.get_atomic_virial()
assert atomic_virial / atomic_virial.unit == pytest.approx(
-11661.677650154408)
atomic_pressure = computer.get_atomic_pressure()
assert atomic_pressure / atomic_pressure.unit == pytest.approx(
-86.95921953101447)
molecular_virial = computer.get_molecular_virial(state.getForces())
assert molecular_virial / molecular_virial.unit == pytest.approx(
-5418.629781093525)
molecular_pressure = computer.get_molecular_pressure(state.getForces())
assert molecular_pressure / molecular_pressure.unit == pytest.approx(
-539.0081647715243)
def platform(name):
return [
openmm.Platform.getPlatformByName(name),
dict(Precision='mixed') if name == 'CUDA' else dict()
]
integrator = openmm.LangevinIntegrator(temp, 0.1 / unit.femtoseconds,
1.0 * unit.femtosecond)
system.addForce(openmm.MonteCarloBarostat(1 * unit.atmospheres, temp, 20))
simulation = app.Simulation(topology, system, integrator,
*platform(simulation_platform))
simulation.context.setPositions(modeller.getPositions())
simulation.context.setVelocitiesToTemperature(temp)
computer = atomsmm.PressureComputer(system, topology,
*platform(pressure_computer_platform))
reporter = atomsmm.ExtendedStateDataReporter(stdout,
100,
step=True,
speed=True,
potentialEnergy=True,
temperature=True,
density=True,
atomicPressure=(not rigid_water),
molecularPressure=True,
pressureComputer=computer,
extraFile='properties.csv')
simulation.reporters.append(reporter)
simulation.minimizeEnergy()
simulation.step(100000)
integrator = atomsmm.integrators.Langevin_R_Integrator(dt,
loops,
temp,
gamma,
has_memory=True)
simulation = openmm.app.Simulation(pdb.topology, respa_system, integrator,
platform, properties)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(temp, seed)
computer = atomsmm.PressureComputer(
openmm_system,
pdb.topology,
# openmm.Platform.getPlatformByName('CPU'),
openmm.Platform.getPlatformByName('CUDA'),
dict(Precision='mixed', DeviceIndex=args.secdev),
temperature=temp)
dataReporter = atomsmm.ExtendedStateDataReporter(
stdout,
reportInterval,
separator=',',
step=True,
potentialEnergy=True,
kineticEnergy=True,
# totalEnergy=True,
temperature=True,
# atomicVirial=True,
atomicPressure=True,
loops,
temp,
tau,
gamma,
L=args.L)
simulation = openmm.app.Simulation(pdb.topology, respa_system, integrator,
platform, properties)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(temp, seed)
computer = atomsmm.PressureComputer(
openmm_system,
pdb.topology,
platform
if args.secdev is None else openmm.Platform.getPlatformByName('CUDA'),
properties if args.secdev is None else dict(Precision='mixed',
DeviceIndex=args.secdev),
temperature=temp,
)
dataReporter = atomsmm.ExtendedStateDataReporter(stdout,
reportInterval,
separator=',',
step=True,
potentialEnergy=True,
temperature=True,
atomicPressure=True,
molecularPressure=True,
pressureComputer=computer,
speed=True,
