Python System.monitorsの例

コード例 #1

ファイル: mtsmc.py プロジェクト: michellab/SireTests

system_qmff = system.forceFields().forceField(qmff.ID())

new_molpro.addToQM(system_qmff.molecules(qmff.groups().qm()))
new_molpro.addToMM(system_qmff.molecules(qmff.groups().mm()),
                   {new_molpro.parameters().coulomb(): "charges"})

print("QM energy = %f, new molproff = %f" % \
            ( system.forceFields().forceField(qmff.ID()).energy(),
              new_molpro.energy() ))

qmff.change(system.forceFields().molecules())

print("qmff == %f" % qmff.energy())

# get the RDFs
rdfmonitor = system.monitors().monitor(Symbol("RDF"))

rdf = rdfmonitor.getRDF(oxygen, oxygen)

print("OXYGEN-OXYGEN")

for point in rdf.normalise():
    print("%f  %f" % point)

print("\nOXYGEN-HYDROGEN")

rdf = rdfmonitor.getRDF(oxygen, hydrogen)

for point in rdf.normalise():
    print("%f  %f" % point)

コード例 #2

ファイル: mtsmc.py プロジェクト: Alwnikrotikz/sire

new_molpro.setMolproExe(qmff.molproExe())
new_molpro.setEnergyOrigin(qmff.energyOrigin())

system_qmff = system.forceFields().forceField(qmff.ID())

new_molpro.addToQM(system_qmff.molecules(qmff.groups().qm()))
new_molpro.addToMM(system_qmff.molecules(qmff.groups().mm()), {new_molpro.parameters().coulomb(): "charges"})

print("QM energy = %f, new molproff = %f" % (system.forceFields().forceField(qmff.ID()).energy(), new_molpro.energy()))

qmff.change(system.forceFields().molecules())

print("qmff == %f" % qmff.energy())

# get the RDFs
rdfmonitor = system.monitors().monitor(Symbol("RDF"))

rdf = rdfmonitor.getRDF(oxygen, oxygen)

print("OXYGEN-OXYGEN")

for point in rdf.normalise():
    print("%f  %f" % point)

print("\nOXYGEN-HYDROGEN")

rdf = rdfmonitor.getRDF(oxygen, hydrogen)

for point in rdf.normalise():
    print("%f  %f" % point)

コード例 #3

ファイル: mtsmc_harmonic.py プロジェクト: michellab/SireTests

system = System(groups, ffields, monitors)

mc = RigidBodyMC(UniformSampler(solute))

mc.setTemperature(25 * celsius)
mc.setMaximumTranslation(0.3 * angstrom)

#for i in range(0,50):
#    moves = system.run(mc, 10000)
#
#    mc = moves.moves()[0].clone()
#    print "%d accepted, %d rejected, ratio = %f %%" % \
#             (mc.nAccepted(), mc.nRejected(), 100 * mc.acceptanceRatio())
#
#    print system.monitors().monitor(ffields.total()).average()

mtsmc = MTSMC(mc, e_fast.function(), 500)
mtsmc.setEnergyComponent(e_slow.function())

for i in range(0, 5000):
    moves = system.run(mtsmc, 20)

    mtsmc = moves.moves()[0].clone()
    print("%d accepted, %d rejected, ratio = %f %%" % \
             (mtsmc.nAccepted(), mtsmc.nRejected(), 100 * mtsmc.acceptanceRatio()))

    print("AVGENERGY: %f" %
          system.monitors().monitor(ffields.total()).average())
    print("ENERGY: %f" % system.forceFields().energy())
    sys.stdout.flush()

コード例 #4

ファイル: mtsmc_harmonic.py プロジェクト: Alwnikrotikz/sire

system = System(groups, ffields, monitors)

mc = RigidBodyMC( UniformSampler(solute) )

mc.setTemperature( 25 * celsius )
mc.setMaximumTranslation( 0.3 * angstrom )

#for i in range(0,50):
#    moves = system.run(mc, 10000)
#
#    mc = moves.moves()[0].clone()
#    print "%d accepted, %d rejected, ratio = %f %%" % \
#             (mc.nAccepted(), mc.nRejected(), 100 * mc.acceptanceRatio())
#         
#    print system.monitors().monitor(ffields.total()).average()


mtsmc = MTSMC(mc, e_fast.function(), 500)
mtsmc.setEnergyComponent(e_slow.function())

for i in range(0,5000):
    moves = system.run(mtsmc, 20)

    mtsmc = moves.moves()[0].clone()
    print("%d accepted, %d rejected, ratio = %f %%" % \
             (mtsmc.nAccepted(), mtsmc.nRejected(), 100 * mtsmc.acceptanceRatio()))
         
    print("AVGENERGY: %f" % system.monitors().monitor(ffields.total()).average())
    print("ENERGY: %f" % system.forceFields().energy())
    sys.stdout.flush()