Python System.monitor示例

示例#1

rdf.add(MolIdx(0) + AtomName("O00"), AtomName("O00"))

rdf2 = RDFMonitor(0 * angstrom, 10 * angstrom, 0.05 * angstrom)
rdf2.add(MolIdx(0) + AtomName("O00"), AtomName("H01"))
rdf2.add(MolIdx(0) + AtomName("O00"), AtomName("H02"))

system.add(cljff)
system.add("O-O RDF", rdf)
system.add("O-H RDF", rdf2)

t.start()
system.collectStats()

ms = t.elapsed()

print("Collecting stats took %d ms" % ms)

rdf = system.monitor(MonitorName("O-O RDF"))

print("\nO-O RDF")

for i in range(0, rdf.nBins()):
    print(rdf[i].middle().to(angstrom), rdf[i].value())

rdf = system.monitor(MonitorName("O-H RDF"))

print("\nO-H RDF")

for i in range(0, rdf.nBins()):
    print(rdf[i].middle().to(angstrom), rdf[i].value())

示例#2

文件： movermove-abcd.py 项目： Alwnikrotikz/sire

#              output="BOND-A1A2.dat")
#histoAnalysis(nbins=nbins,
#              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
#              values=system.monitor( MonitorName("bond23") ).accumulator().values(),
#              mode="bond",
#              output="BOND-A2A3.dat")
#histoAnalysis(nbins=nbins,
#              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
#              values=system.monitor( MonitorName("bond34") ).accumulator().values(),
#              mode="bond",
#              output="BOND-A3A4.dat")
#histoAnalysis(nbins=nbins,
#              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
#              values=system.monitor( MonitorName("theta123") ).accumulator().values(),
#              mode="angle",
#              output="ANGLE-A1A2A3.dat")
#histoAnalysis(nbins=nbins,
#              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
#              values=system.monitor( MonitorName("theta234") ).accumulator().values(),
#              mode="angle",
#              output="ANGLE-A2A3A4.dat")
histoAnalysis(nbins=nbins,
              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
              values=list(system.monitor( MonitorName("phi1234") ).accumulator().values()),
              mode="angle",
              output="DIHEDRAL-A1A2A3A4.dat")


#**  Output the trajectory
#system.monitor( MonitorName("trajectory") ).writeToDisk("outputXXXXXX.pdb")

示例#3

文件： energymonitor.py 项目： michellab/SireTests

                           .setProperty("b-factor",beta_ljnrg).molecule().commit()

            total_mol = total_mol.atom(atoms[j].index()).edit() \
                                 .setProperty("b-factor",beta_total).molecule().commit()

        coul_group.update(coul_mol)
        lj_group.update(lj_mol)
        total_group.update(total_mol)

    print("Total energies: %f  %f  %f" % (cnrg, ljnrg, cnrg + ljnrg))

    PDB().write(coul_group, "test_coul_%0004d.pdb" % id)
    PDB().write(lj_group, "test_lj_%0004d.pdb" % id)
    PDB().write(total_group, "test_total_%0004d.pdb" % id)


print("Running a simulation...")

for i in range(1, 11):
    system = moves.move(system, 2000, True)

    nrgmon = system.monitor(MonitorName("solute_shell"))

    PDB().write(system.molecules(), "test_sim_%0004d.pdb" % i)

    system.clearStatistics()

    print("Step %d of 10: Energy = %s" % (i, system.energy()))

    view(nrgmon, i)

示例#4

文件： rdf.py 项目： Alwnikrotikz/sire

rdf2 = RDFMonitor( 0*angstrom, 10*angstrom, 0.05*angstrom )
rdf2.add( MolIdx(0) + AtomName("O00"), AtomName("H01") )
rdf2.add( MolIdx(0) + AtomName("O00"), AtomName("H02") )

system.add(cljff)
system.add("O-O RDF", rdf)
system.add("O-H RDF", rdf2)

t.start()
system.collectStats()

ms = t.elapsed()

print("Collecting stats took %d ms" % ms)

rdf = system.monitor( MonitorName("O-O RDF") )

print("\nO-O RDF")

for i in range(0,rdf.nBins()):
    print(rdf[i].middle().to(angstrom), rdf[i].value())

rdf = system.monitor( MonitorName("O-H RDF") )

print("\nO-H RDF")

for i in range(0,rdf.nBins()):
    print(rdf[i].middle().to(angstrom), rdf[i].value())

示例#5

文件： testmonitors.py 项目： michellab/SireTests

t = QTime()
t.start()

# Run the simulation
for i in range(0, nblocks):
    print("Running nmove...")
    t.restart()
    system = moves.move(system, nmoves, True)
    print("...took %d ms" % t.elapsed())

print("Analysis...")
# make an histogram...
nbins = 31
histoAnalysis(
    nbins=nbins,
    values=list(system.monitor(MonitorName("bond12")).accumulator().values()),
    mode="bond",
    output="BOND-A1A2.dat")

histoAnalysis(
    nbins=nbins,
    values=list(system.monitor(MonitorName("bond23")).accumulator().values()),
    mode="bond",
    output="BOND-A2A3.dat")

histoAnalysis(nbins=nbins,
              values=list(
                  system.monitor(
                      MonitorName("angle123")).accumulator().values()),
              mode="angle",
              output="ANGLE-A1A2A3.dat")

示例#6

文件： energymonitor.py 项目： Alwnikrotikz/sire

            lj_mol = lj_mol.atom(atoms[j].index()).edit() \
                           .setProperty("b-factor",beta_ljnrg).molecule().commit()

            total_mol = total_mol.atom(atoms[j].index()).edit() \
                                 .setProperty("b-factor",beta_total).molecule().commit()

        coul_group.update(coul_mol)
        lj_group.update(lj_mol)
        total_group.update(total_mol)

    print("Total energies: %f  %f  %f" % (cnrg, ljnrg, cnrg+ljnrg))

    PDB().write(coul_group, "test_coul_%0004d.pdb" % id)
    PDB().write(lj_group, "test_lj_%0004d.pdb" % id)
    PDB().write(total_group, "test_total_%0004d.pdb" % id)

print("Running a simulation...")

for i in range(1,11):
    system = moves.move(system, 2000, True)

    nrgmon = system.monitor( MonitorName("solute_shell") )

    PDB().write(system.molecules(), "test_sim_%0004d.pdb" % i)

    system.clearStatistics()

    print("Step %d of 10: Energy = %s" % (i, system.energy()))

    view(nrgmon, i)

示例#7

            break
    moves = SameMoves(solute_mover)

print("Production")
for i in range(0,nblocks):
    print("Running block %d " % i)
    system = moves.move(system, nmoves, True)
#sys.exit(-1)
print("Analysis...")
# make an histogram...
nbins=31

for bond in var_bonds:
    bmonitor = "b_%s_%s" % (bond.atom0().value(),bond.atom1().value()) 
    histoAnalysis(nbins=nbins,
                  values=list(system.monitor( MonitorName(bmonitor) ).accumulator().values()),
                  avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
                  mode="bond",
                  output="BOND-%s.dat" % bmonitor)


for angle in var_angles:
    amonitor = "a_%s_%s_%s" % (angle.atom0().value(), 
                               angle.atom1().value(),
                               angle.atom2().value() ) 
    histoAnalysis(nbins=nbins,
                  values=list(system.monitor( MonitorName(amonitor) ).accumulator().values()),
                  avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
                  mode="angle",
                  output="ANGLE-%s.dat" % amonitor)

示例#8

文件： testmonitors.py 项目： Alwnikrotikz/sire

t = QTime()
t.start()

# Run the simulation
for i in range(0,nblocks):
   print("Running nmove...")
   t.restart()
   system = moves.move(system, nmoves, True)
   print("...took %d ms" % t.elapsed())

print("Analysis...")
# make an histogram...
nbins=31
histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("bond12") ).accumulator().values()),
              mode="bond",
              output="BOND-A1A2.dat")

histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("bond23") ).accumulator().values()),
              mode="bond",
              output="BOND-A2A3.dat")

histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("angle123") ).accumulator().values()),
              mode="angle",
              output="ANGLE-A1A2A3.dat")

#**  Output the trajectory
#system.monitor( MonitorName("trajectory") ).writeToDisk("outputXXXXXX.pdb")

示例#9

文件： movermove-triatomic.py 项目： michellab/SireTests

e_total = system.totalComponent()
system.add( "total_energy", MonitorComponent(e_total, Average()) )

#system.add( "trajectory", TrajectoryMonitor(system[MGIdx(0)]), 1 )

# Run the simulation
for i in range(0,nblocks):
    print("Running nmove...")
    system = moves.move(system, nmoves, True)

print("Analysis...")
# make an histogram...
nbins=31
histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("bond12") ).accumulator().values()),
              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
              mode="bond",
              output="BOND-A1A2.dat")
histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("bond23") ).accumulator().values()),
              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
              mode="bond",
              output="BOND-A2A3.dat")
histoAnalysis(nbins=nbins,
              values=list(system.monitor( MonitorName("angle123") ).accumulator().values()),
              avgnrg = system.monitor( MonitorName("total_energy") ).accumulator().average(),
              mode="angle",
              output="ANGLE-A1A2A3.dat")

#**  Output the trajectory