def nanoTubeTest():
print "\nLoading configuration with sp2 bonded carbon (nanotube)"
a = NetCDFTrajectory("sp2carbon-nanotube.nc").GetListOfAtoms()
a.SetCartesianMomenta(zeros((len(a), 3), Float))
potential = BrennerPotential()
a.SetCalculator(potential)
print "Calculating forces"
f = a.GetCartesianForces()
print "Loading correct forces"
target = load(open("sp2carbon-nanotube-forces.pickle"))
print "Comparing forces"
for i in range(len(a)):
for j in (0, 1, 2):
ReportTest("Force[%d,%d]" % (i, j),
f[i, j],
target[i, j],
1e-3,
silent=True)
print "Testing energy conservation"
#dyn = PredictorCorrector(a, 0.2) #bad result for energy conservation
dyn = VelocityVerlet(a, 0.2 * femtosecond)
dyn.Run(100)
step = 100
etot = a.GetPotentialEnergy() + a.GetKineticEnergy()
print "Total energy after %4.d steps: %.8f" % (
step, a.GetPotentialEnergy() + a.GetKineticEnergy())
for i in range(10):
dyn.Run(100)
step += 100
print "Total energy after %4.d steps: %.8f" % (
step, a.GetPotentialEnergy() + a.GetKineticEnergy())
ReportTest("Approximate energy conservation",
a.GetPotentialEnergy() + a.GetKineticEnergy(),
etot,
0.3,
silent=True)
from Asap.Utilities import BrennerImport
# read the coordinates and the types of atoms from a
# brenner dot d file:
brenner = BrennerImport.BrennerImport()
brenner.initCoord("coord.d")
a=brenner.GetListOfAtoms()
# initialize the Brenner Potential with automatically adapting cube size
potential = BrennerPotential(True)
# set accuracy
potential.SetRll(2.5)
#define the cube size (You can only set the cube size, if you created the potential using BrennerPotential(False))
#potential.SetCubeSize(brenner.GetCubeSize())
a.SetCalculator(potential)
#step size 0.2 femtoseconds
dyn = VelocityVerlet(a, 0.2*femtosecond)
step = 0;
etot = a.GetPotentialEnergy() + a.GetKineticEnergy()
for i in range(6):
dyn.Run(100)
step+=100
print "Total energy after %4.d steps: %.8f"%(step,a.GetPotentialEnergy()+a.GetKineticEnergy())
#write xmol.d log file
potential.WriteXmol(step, 0.2*femtosecond);
df = max(fabs(f.flat - oldf.flat))
print "Maximal deviation: Energy", de, " Force", df
ReportTest("Max force error", df, 0.0, 1e-11)
ReportTest("Max energy error", de, 0.0, 1e-11)
del olde, oldf
else:
print "WARNING: No self-check database found, creating it."
cPickle.dump((e, f), open(selfcheckfilename, "w"))
del e,f,atoms
ReportTest.Summary(exit=1)
print "Preparing to run Verlet dynamics (free boundaries)."
atoms = ListOfAtoms(initial, periodic=(0,0,0))
atoms.SetCalculator(EMT())
dynamics = VelocityVerlet(atoms, 5*femtosecond)
print "Running Verlet dynamics."
startcpu, startwall = time.clock(), time.time()
dynamics.Run(timesteps)
vfcpu, vfwall = time.clock() - startcpu, time.time() - startwall
vffraction = vfcpu/vfwall
sys.stderr.write("\n")
print "Verlet dynamics done."
del dynamics, atoms
print "Preparing to run Verlet dynamics (periodic boundaries)."
atoms = ListOfAtoms(initial, periodic=(1,1,1))
atoms.SetCalculator(EMT())
dynamics = VelocityVerlet(atoms, 5*femtosecond)
from cPickle import *
from Numeric import *
from Asap.testtools import ReportTest
PrintVersion(1)
data = load(file("testVerlet.pickle"))
init_pos = array(data["initial"])
init_pos.shape = (-1, 3)
init_box = array(data["box"])
init_box.shape = (3, 3)
atoms = ListOfAtoms(positions=init_pos, cell=init_box)
atoms.SetAtomicNumbers(47)
atoms.SetCalculator(MonteCarloEMT())
dyn = VelocityVerlet(atoms, 2 * femtosecond)
for i in range(20):
dyn.Run(10)
epot = atoms.GetPotentialEnergy() / len(atoms)
ekin = atoms.GetKineticEnergy() / len(atoms)
print "E_pot = %-12.5f E_kin = %-12.5f E_tot = %-12.5f" % (epot, ekin,
epot + ekin)
final_pos = array(data["final"])
diff = max(abs(atoms.GetCartesianPositions().flat - final_pos))
print "Maximal deviation of positions:", diff
ReportTest("Maximal deviation of positions", diff, 0, 1e-9)
diff = max(abs(atoms.GetStresses().flat - array(data["stress"])))
print "Maximal deviation of stresses:", diff