def maketraj(atoms, t, nstep):
e = [atoms.get_potential_energy()]
dyn = VelocityVerlet(atoms, 5*units.fs)
for i in range(nstep):
dyn.run(10)
e.append(atoms.get_potential_energy())
if t is not None:
t.write()
return e
def maketraj(atoms, t, nstep):
e = [atoms.get_potential_energy()]
dyn = VelocityVerlet(atoms, 5 * units.fs)
for i in range(nstep):
dyn.run(10)
e.append(atoms.get_potential_energy())
if t is not None:
t.write()
return e
def twoAtomForce():
print "\nRunning LJ twoAtomForce"
elements = [29]
epsilon = [0.15]
sigma = [2.7]
atoms=Atoms(positions=[(0.0, 0.0, 0.0),(0.0, 0.0, 2.0)],
symbols="Cu2")
atoms.set_calculator(LennardJones(elements, epsilon, sigma, -1.0, False))
result = atoms.get_potential_energy()
r = atoms.get_positions()
r.flat[:] += 0.06 * np.sin(np.arange(3*len(atoms)))
atoms.set_positions(r)
resA, resB = atoms.get_forces() ;
storedForces = [ -1.15732425, 13.10743025, -258.04517252 ]
for a in range(1,3):
ReportTest((" Simple force test dimension %d" % a), resA[a],
storedForces[a], 1e-8, silent=Silent)
print " Running Verlet dynamics (%s)" % ("Cu",)
dyn = VelocityVerlet(atoms, 2*units.fs)
dyn.run(100)
etot1 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
dyn.run(1000)
etot2 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
ReportTest((" Energy conservation (%s)" % ("Cu",)), etot1, etot2, 1.0, silent=Silent)
epot = atoms.get_potential_energies()
stress = atoms.get_stresses()
e = []
s = []
j = 0
for i in range(0, len(atoms), 100):
e.append(epot[i])
s.append(stress[i,j])
j = (j + 1) % 6
print " e"+"Cu"+" =", repr(e)
print " s"+"Cu"+" =", repr(s)
def dotest(atoms, nsteps, ampl, name):
print "Potential energy", atoms.get_potential_energy() / len(atoms)
r = atoms.get_positions()
r.flat[:] += ampl * sin(arange(3*len(atoms)))
atoms.set_positions(r)
print "Potential energy", atoms.get_potential_energy() / len(atoms)
print "Running Verlet dynamics (%s)" % (name,)
dyn = VelocityVerlet(atoms, 2*femtosecond)
etot1 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
dyn.run(nsteps)
etot2 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
ReportTest(("Energy conservation (%s)" % (name,)), etot1, etot2, 1.0)
print etot1, etot2
epot = atoms.get_potential_energies()
stress = atoms.get_stresses()
if firsttime:
print "Reporting energies and stresses"
e = []
s = []
j = 0
for i in range(0, len(atoms), 100):
e.append(epot[i])
s.append(stress[i,j])
j = (j + 1) % 6
print >> out, "e"+name+" =", repr(e)
print >> out, "s"+name+" =", repr(s)
else:
print "Testing energies and stresses"
j = 0
eres=getattr(potResults, "e"+name)
sres=getattr(potResults, "s"+name)
for i in range(len(atoms)/100):
ReportTest(("%s energy %d" % (name, i*100)),
epot[i*100], eres[i], 1e-8, silent=True)
ReportTest(("%s stress %d" % (name, i*100)),
stress[i*100, j], sres[i], 1e-8, silent=True)
j = (j + 1) % 6
def twoAtomForce():
print "\nRunning LJ twoAtomForce"
elements = [29]
epsilon = [0.15]
sigma = [2.7]
atoms = Atoms(positions=[(0.0, 0.0, 0.0), (0.0, 0.0, 2.0)], symbols="Cu2")
atoms.set_calculator(LennardJones(elements, epsilon, sigma, -1.0, False))
result = atoms.get_potential_energy()
r = atoms.get_positions()
r.flat[:] += 0.06 * np.sin(np.arange(3 * len(atoms)))
atoms.set_positions(r)
resA, resB = atoms.get_forces()
storedForces = [-1.15732425, 13.10743025, -258.04517252]
for a in range(1, 3):
ReportTest((" Simple force test dimension %d" % a),
resA[a],
storedForces[a],
1e-8,
silent=Silent)
print " Running Verlet dynamics (%s)" % ("Cu", )
dyn = VelocityVerlet(atoms, 2 * units.fs)
dyn.run(100)
etot1 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
dyn.run(1000)
etot2 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
ReportTest((" Energy conservation (%s)" % ("Cu", )),
etot1,
etot2,
1.0,
silent=Silent)
epot = atoms.get_potential_energies()
stress = atoms.get_stresses()
e = []
s = []
j = 0
for i in range(0, len(atoms), 100):
e.append(epot[i])
s.append(stress[i, j])
j = (j + 1) % 6
print " e" + "Cu" + " =", repr(e)
print " s" + "Cu" + " =", repr(s)
def Compare(name, atoms, observer, ref, interval=4):
dyn = VelocityVerlet(atoms, 5*units.fs)
dyn.attach(observer, interval=interval)
r = []
for i in range(50):
dyn.run(5)
epot = atoms.get_potential_energy() / len(atoms)
ekin = atoms.get_kinetic_energy() / len(atoms)
r.append([epot, ekin, epot+ekin])
r = array(r)
diff = r - ref
maxdiff = diff.max()
print "Maximal difference is", maxdiff
ReportTest(name, maxdiff, 0.0, 1e-6)
z = init.get_positions()[:,2]
fixedatoms = np.less(z, 0.501*z.max())
print len(init), sum(fixedatoms)
MaxwellBoltzmannDistribution(init, 6000*units.kB)
init.set_tags(fixedatoms)
else:
init = None
print
print "Running simulation with Filter"
atoms1 = MakeParallelAtoms(init, cpulayout)
atoms1.arrays['r_init'] = atoms1.get_positions()
atoms1.set_calculator(EMT())
atoms1a = Filter(atoms1, mask=np.logical_not(atoms1.get_tags()))
dyn = VelocityVerlet(atoms1a, 3*units.fs)
dyn.run(100)
print
print "Running simulation with Asap's FixAtoms"
atoms2 = MakeParallelAtoms(init, cpulayout)
atoms2.arrays['r_init'] = atoms2.get_positions()
atoms2.set_calculator(EMT())
atoms2.set_constraint(FixAtoms(mask=atoms2.get_tags()))
dyn = VelocityVerlet(atoms2, 3*units.fs)
dyn.run(100)
print
print "Running Langevin simulation with Asap's FixAtoms"
atoms4 = MakeParallelAtoms(init, cpulayout)
from numpy import * from asap3 import Atoms, EMT, units from ase.visualize.primiplotter import * from ase.lattice.cubic import FaceCenteredCubic from asap3.md.verlet import VelocityVerlet # Create the atoms atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False) # Give the first atom a non-zero momentum atoms[0].set_momentum(array([0, -11.3, 0])) # Associate the EMT potential with the atoms atoms.set_calculator(EMT()) # Now do molecular dynamics, printing kinetic, potential and total # energy every ten timesteps. dyn = VelocityVerlet(atoms, 5.0*units.fs) # Set up a plotter plotter = PrimiPlotter(atoms) plotter.set_output(X11Window()) # Attach it to the dynamics, so it is informed every 25'th time a # timestep is made. dyn.attach(plotter.plot, interval=25) # Now do 1000 timesteps. dyn.run(1000) print "The output is in the NetCDF file TrajectoryMD-output.traj"
if line[:7] == "cpu MHz":
cpumhz = line
break
except:
print "Cannot get CPU info from /proc/cpuinfo"
logger.write(cpumhz)
logger.write(modelname)
logger.write(asapversion + "\n")
logger.write("Number of threads: " + str(nthreads) + "\n")
atoms300 = MakeCu()
atoms = Atoms(atoms300)
atoms.set_calculator(EMT())
dyn = VelocityVerlet(atoms, 5 * units.fs)
Timing("Ver300", dyn.run, 50, len(atoms))
atoms = MakeCu(1000)
dyn = VelocityVerlet(atoms, 5 * units.fs)
Timing("Ver1000", dyn.run, 50, len(atoms))
atoms = Atoms(atoms300)
atoms.set_calculator(EMT())
dyn = Langevin(atoms, 5 * units.fs, 300 * units.kB, 0.001)
Timing("Langevin", dyn.run, 50, len(atoms))
atoms = Atoms(atoms300)
atoms.set_calculator(EMT())
dyn = NPT(atoms, 5 * units.fs, 300 * units.kB, 0, 25 * units.fs,
(75 * units.fs)**2 * 140 * units.GPa)
ReportTest(name, maxdiff, 0.0, 1e-6)
print_version(1)
print "Making initial system"
iniatoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(10,5,5), symbol="Cu", pbc=(1,1,0))
iniatoms.set_calculator(EMT())
inidyn = Langevin(iniatoms, 5*units.fs, 450*units.kB, 0.05)
inidyn.run(100)
print "Temperature is now", iniatoms.get_kinetic_energy() / (1.5*units.kB*len(iniatoms)), "K"
print "Making reference simulation"
refatoms = Atoms(iniatoms)
refatoms.set_calculator(EMT())
dyn = VelocityVerlet(refatoms, 5*units.fs)
ref = []
for i in range(50):
dyn.run(5)
epot = refatoms.get_potential_energy() / len(refatoms)
ekin = refatoms.get_kinetic_energy() / len(refatoms)
ref.append([epot, ekin, epot+ekin])
ref = array(ref)
print "Testing RestrictedCNA"
atoms = Atoms(iniatoms)
atoms.set_calculator(EMT())
cna = RestrictedCNA(atoms)
Compare("RestrictedCNA", atoms, cna.analyze, ref)
from asap3 import Atoms, EMT, units
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].set_momentum(array([0, -11.3, 0]))
print "Kinetic energies of all atoms:"
p = atoms.get_momenta()
kinenergies = 0.5 * (p * p).sum(1) / atoms.get_masses()
print kinenergies
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
print ""
print "Energy per atom:"
print " %15s %15s %15s" % ("Pot. energy", "Kin. energy", "Total energy")
for i in range(25):
dyn.run(10)
epot = atoms.get_potential_energy()/len(atoms)
ekin = atoms.get_kinetic_energy()/len(atoms)
print "%15.5f %15.5f %15.5f" % (epot, ekin, epot+ekin)
atoms = FaceCenteredCubic(size=(2,10,10), symbol="Cu", pbc=False,
latticeconstant = 3.5)
else:
atoms = None
if isparallel:
atoms = MakeParallelAtoms(atoms, cpulayout)
atoms.set_calculator(asap3.EMT())
natoms = atoms.get_number_of_atoms()
ReportTest("Number of atoms", natoms, 800, 0)
# Make a small perturbation of the momenta
atoms.set_momenta(1e-6 * random.random([len(atoms), 3]))
print "Initializing ..."
predyn = VelocityVerlet(atoms, 0.5)
try:
predyn.run(2500)
except:
print atoms.arrays['positions']
print atoms.arrays['momenta']
print atoms.arrays['momenta'].shape
print atoms.get_masses()
print atoms.get_masses().shape
raise
initr = atoms.get_positions()
initp = atoms.get_momenta()
for nthreads in threads:
try:
AsapThreads(nthreads)
except ValueError:
break
maxthread = nthreads
for natoms in sizes:
print "Timing with %i atoms (%i threads)" % (natoms, nthreads)
blocksize = int(np.ceil((natoms/4)**(1./3.)))
atoms = FaceCenteredCubic(symbol='Cu', size=(blocksize,blocksize,blocksize), pbc=False)
print "Creating block with %i atoms, cutting to %i atoms" % (len(atoms), natoms)
atoms = atoms[:natoms]
assert len(atoms) == natoms
atoms.set_calculator(EMT())
MaxwellBoltzmannDistribution(atoms, 2 * T * units.kB)
dyn = VelocityVerlet(atoms, 5*units.fs)
ptsteps = int(laststeps * (0.1 * targettime / lasttime) * lastsize / natoms)
if ptsteps < 100:
ptsteps = 100
print "Running pre-timing (%i steps)..." % (ptsteps,)
t1 = time.time()
dyn.run(ptsteps - 50)
MaxwellBoltzmannDistribution(atoms, (2 * T - atoms.get_temperature()) * units.kB)
dyn.run(50)
t1 = time.time() - t1
steps = int(ptsteps * targettime / t1)
if steps < 200:
steps = 200
print "Temperature is %.1f K" % (atoms.get_temperature(),)
print "Running main timing (%i steps)" % (steps,)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
from numpy import *
from asap3 import Atoms, EMT, units
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3, 3, 3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].set_momentum(array([0, -11.3, 0]))
print "Kinetic energies of all atoms:"
p = atoms.get_momenta()
kinenergies = 0.5 * (p * p).sum(1) / atoms.get_masses()
print kinenergies
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0 * units.fs)
print ""
print "Energy per atom:"
print " %15s %15s %15s" % ("Pot. energy", "Kin. energy", "Total energy")
for i in range(25):
dyn.run(10)
epot = atoms.get_potential_energy() / len(atoms)
ekin = atoms.get_kinetic_energy() / len(atoms)
print "%15.5f %15.5f %15.5f" % (epot, ekin, epot + ekin)
import sys
if len(sys.argv) == 2:
arg = sys.argv[1]
else:
arg = 'Wrong number of arguments.'
if arg == 'EMT':
filename = 'small_EMT.dat'
elif arg == 'EMT2013':
filename = 'small_EMT2013.dat'
else:
print __doc__
sys.exit(1)
T = 450
atoms = FaceCenteredCubic(size=(10, 10, 10), symbol='Cu', pbc=False)
if arg == 'EMT':
atoms.set_calculator(EMT())
else:
atoms.set_calculator(EMT2013(EMT2013_parameters))
print "Setting temperature:", T, "K"
MaxwellBoltzmannDistribution(atoms, 2 * T * units.kB)
Stationary(atoms)
dyn1 = Langevin(atoms, 2 * units.fs, temperature=T * units.kB, friction=0.05)
dyn1.run(200)
dyn = VelocityVerlet(atoms, 3 * units.fs, logfile=filename, loginterval=25)
dyn.run(10000000) # 10^7 timesteps is 3 ns.
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."
atoms = Atoms(initial)
atoms.set_calculator(EMT())
dynamics = VelocityVerlet(atoms, 5*units.fs)
print "Running Verlet dynamics."
startcpu, startwall = time.clock(), time.time()
dynamics.run(timesteps)
vcpu, vwall = time.clock() - startcpu, time.time() - startwall
vfraction = vcpu/vwall
sys.stderr.write("\n")
print "Verlet dynamics done."
del dynamics, atoms
print "Preparing to run Langevin dynamics."
atoms = Atoms(initial)
atoms.set_calculator(EMT())
dynamics = Langevin(atoms, 5*units.fs, 400*units.kB, 0.001)
def dynamicsTest(size, before, steps, v0, rCut, nonSense):
print "\n\nStarting LJ dynamicsTest with "
print " cube of size %d" % size
print " time before measurement start %d*1*femtoseconds" % before
print " measuring time %d*femtoseconds" % steps
print " add v0 %d" % (v0 == 1)
print " rCut %d" % rCut
print " 3 kinds of atoms %s" % (nonSense == 1)
start = time()
nsteps = steps
#Warning: numbers and constants are not supposed to make sense or to be correct!!
# they're only here to assure that the program handles the input correctly
if nonSense:
elements = [29, 79, 39]
epsilon = [0.15, 0.00, 0.00, 0.10, 0.25, 0.00, 0.31, 0.60, 0.15]
sigma = [2.7, 0.00, 0.00, 1.90, 2.7, 0.00, 2.20, 1.50, 2.7]
atoms = L1_2([[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(size, size, size),
element=("Cu", "Au"),
periodic=(1, 0, 1),
debug=0,
latticeconstant=3.95)
atoms.set_calculator(LennardJones(elements, epsilon, sigma, rCut, v0))
else:
elements = [29]
epsilon = [0.15]
sigma = [2.7]
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(size, size, size),
symbol="Cu",
pbc=(1, 0, 1),
debug=0,
latticeconstant=1.09 * sigma[0] * 1.41)
atoms.set_calculator(LennardJones(elements, epsilon, sigma, rCut, v0))
r = atoms.get_positions()
r.flat[:] += 0.06 * np.sin(np.arange(3 * len(atoms)))
atoms.set_positions(r)
print " Running Verlet dynamics (%s)" % ("Cu", )
dyn = VelocityVerlet(atoms, 1 * units.fs)
dyn.run(before)
etot1 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
for i in range(nsteps / 10):
dyn.run(10)
#print atoms.get_potential_energy()/len(atoms), atoms.get_kinetic_energy()/len(atoms), (atoms.get_potential_energy() + atoms.get_kinetic_energy())/len(atoms)
etot2 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
ReportTest((" Energy conservation (%s)" % ("Cu", )),
etot1,
etot2,
2,
silent=Silent)
print "Before: ", etot1, " now: ", etot2, " diff= ", (etot1 - etot2)
epot = atoms.get_potential_energies()
stress = atoms.get_stresses()
print " Reporting energies and stresses"
e = []
s = []
j = 0
for i in range(0, len(atoms), 100):
e.append(epot[i])
s.append(stress[i, j])
j = (j + 1) % 6
print " e" + "Cu" + " =", repr(e)
print " s" + "Cu" + " =", repr(s)
end = time()
print " ++++ Test runtime of the LJ dynamicsTest was %d seconds ++++\n\n" % (
end - start)
if 1:
sumstress = np.zeros(6, np.float)
for s in stress:
sumstress += s
totalstress = atoms.get_stress()
for i in range(6):
ReportTest("Sum of stresses (%d)" % (i, ),
sumstress[i] / len(atoms), totalstress[i],
abs(0.01 * totalstress[i]))
from ase.visualize.primiplotter import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].momentum = array([0, -11.3, 0])
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
# Set up a plotter
plotter = PrimiPlotter(atoms)
plotter.set_output(X11Window()) # Plot in X11 window on the user's screen
plotter.set_output(JpegFile("a")) # Save as GIF files
# plotter.set_output(PostScriptFile("a")) # Save as PS files
# Attach it to the dynamics, so it is informed every 25'th time a
# timestep is made.
dyn.attach(plotter.plot, interval=25)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the NetCDF file TrajectoryMD-output.traj"
from numpy import *
from asap3 import Atoms, EMT, units, PickleTrajectory
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].set_momentum(array([0, -11.3, 0]))
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
# Make a trajectory writing output
trajectory = PickleTrajectory("TrajectoryMD-output.traj", "w", atoms)
# Attach it to the dynamics, so it is informed every fifth time a
# timestep is made.
dyn.attach(trajectory, interval=5)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the NetCDF file TrajectoryMD-output.traj"
frict = 0.001
temp = 100 # K
repeats = 5
# Set up atoms in a regular simple-cubic lattice.
initial = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size = (1,5,5), symbol="Cu", latticeconstant=3.5,
pbc=False, debug=0)
initial.set_calculator(EMT())
ReportTest("Number of atoms", len(initial), 100, 0)
# Make a small perturbation of the momenta
initial.set_momenta(1e-6 * np.random.normal(size=[len(initial), 3]))
print "Initializing (1) ..."
predyn = VelocityVerlet(initial, 0.5)
predyn.run(2500)
initial2 = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size = (4,4,4), symbol="Cu", debug=0)
initial2.set_calculator(EMT())
# Make a small perturbation of the momenta
initial2.set_momenta(1e-6 * np.random.normal(size=[len(initial2), 3]))
print "Initializing (2) ..."
predyn = VelocityVerlet(initial2, 0.5)
predyn.run(2500)
class TemperatureMonitor:
def __init__(self, report):
self.report = report
from asap3.testtools import ReportTest import numpy as np init = FaceCenteredCubic(size=(10,10,10), symbol='Cu', pbc=False) z = init.get_positions()[:,2] fixedatoms = np.less(z, 0.501*z.max()) print len(init), sum(fixedatoms) MaxwellBoltzmannDistribution(init, 2000*units.kB) print print "Running simulation with Filter" atoms1 = Atoms(init) atoms1.set_calculator(EMT()) atoms1a = Filter(atoms1, mask=np.logical_not(fixedatoms)) dyn = VelocityVerlet(atoms1a, 0.5*units.fs) dyn.run(50) r1 = atoms1.get_positions() print print "Running simulation with Asap's FixAtoms" atoms2 = Atoms(init) atoms2.set_calculator(EMT()) atoms2.set_constraint(FixAtoms(mask=fixedatoms)) dyn = VelocityVerlet(atoms2, 0.5*units.fs) dyn.run(50) r2 = atoms2.get_positions() print print "Running simulation with ASE's FixAtoms"
"""
from numpy import *
from asap3 import Atoms, EMT, units, Trajectory
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3, 3, 3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].momentum = array([0, -11.3, 0])
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0 * units.fs)
# Make a trajectory writing output
trajectory = Trajectory("TrajectoryMD-output.traj", "w", atoms)
# Attach it to the dynamics, so it is informed every fifth time a
# timestep is made.
dyn.attach(trajectory, interval=5)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the ASE Trajectory file TrajectoryMD-output.traj"
ReportTest("Max force error", df, 0.0, 1e-11)
ReportTest("Max energy error", de, 0.0, 1e-11)
print e[:20]
print olde[:20]
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."
atoms = Atoms(initial)
atoms.set_calculator(EMT())
dynamics = VelocityVerlet(atoms, 5*units.fs)
print "Running Verlet dynamics."
startcpu, startwall = time.clock(), time.time()
dynamics.run(timesteps)
vcpu, vwall = time.clock() - startcpu, time.time() - startwall
vfraction = vcpu/vwall
sys.stderr.write("\n")
print "Verlet dynamics done."
del dynamics, atoms
print "Preparing to run Langevin dynamics."
atoms = Atoms(initial)
atoms.set_calculator(EMT())
dynamics = Langevin(atoms, 5*units.fs, 400*units.kB, 0.001)
else:
atoms = None
out = file("/dev/null", "w")
if isparallel:
atoms = MakeParallelAtoms(atoms, cpulayout)
nTotalAtoms = atoms.get_number_of_atoms()
else:
nTotalAtoms = len(atoms)
#report()
print "Setting potential"
atoms.set_calculator(OpenKIMcalculator(openkimmodel, allowed='MI_OPBC_F'))
dyn = VelocityVerlet(atoms, 2 * femtosecond)
# if isparallel:
# traj = ParallelNetCDFTrajectory("ptraj.nc", atoms, interval=20)
# else:
# traj = NetCDFTrajectory("ptraj.nc", atoms, interval=20)
# dyn.Attach(traj)
# traj.Update()
print "Number of atoms:", nTotalAtoms
epot = atoms.get_potential_energy() / nTotalAtoms
ekin = atoms.get_kinetic_energy() / nTotalAtoms
etotallist = [epot+ekin]
ekinlist = [ekin]
#report()
from asap3.testtools import ReportTest import numpy as np init = FaceCenteredCubic(size=(10, 10, 10), symbol='Cu', pbc=False) z = init.get_positions()[:, 2] fixedatoms = np.less(z, 0.501 * z.max()) print len(init), sum(fixedatoms) MaxwellBoltzmannDistribution(init, 2000 * units.kB) print print "Running simulation with Filter" atoms1 = Atoms(init) atoms1.set_calculator(EMT()) atoms1a = Filter(atoms1, mask=np.logical_not(fixedatoms)) dyn = VelocityVerlet(atoms1a, 0.5 * units.fs) dyn.run(50) r1 = atoms1.get_positions() print print "Running simulation with Asap's FixAtoms" atoms2 = Atoms(init) atoms2.set_calculator(EMT()) atoms2.set_constraint(FixAtoms(mask=fixedatoms)) dyn = VelocityVerlet(atoms2, 0.5 * units.fs) dyn.run(50) r2 = atoms2.get_positions() print print "Running simulation with ASE's FixAtoms"
if len(sys.argv) == 2:
arg = sys.argv[1]
else:
arg = 'Wrong number of arguments.'
if arg == 'EMT':
filename = 'small_EMT.dat'
elif arg == 'EMT2013':
filename = 'small_EMT2013.dat'
else:
print __doc__
sys.exit(1)
T = 450
atoms = FaceCenteredCubic(size=(10,10,10), symbol='Cu', pbc=False)
if arg == 'EMT':
atoms.set_calculator(EMT())
else:
atoms.set_calculator(EMT2013(EMT2013_parameters))
print "Setting temperature:", T, "K"
MaxwellBoltzmannDistribution(atoms, 2*T*units.kB)
Stationary(atoms)
dyn1 = Langevin(atoms, 2*units.fs, temperature=T*units.kB, friction=0.05)
dyn1.run(200)
dyn = VelocityVerlet(atoms, 3*units.fs, logfile=filename, loginterval=25)
dyn.run(10000000) # 10^7 timesteps is 3 ns.
def dynamicsTest(size, before, steps, v0, rCut, nonSense):
print "\n\nStarting LJ dynamicsTest with "
print " cube of size %d"%size
print " time before measurement start %d*1*femtoseconds"%before
print " measuring time %d*femtoseconds"%steps
print " add v0 %d"%(v0==1)
print " rCut %d"%rCut
print " 3 kinds of atoms %s"%(nonSense==1)
start = time();
nsteps = steps;
#Warning: numbers and constants are not supposed to make sense or to be correct!!
# they're only here to assure that the program handles the input correctly
if nonSense:
elements = [29, 79, 39]
epsilon = [0.15, 0.00, 0.00,
0.10, 0.25, 0.00,
0.31, 0.60, 0.15]
sigma = [2.7 , 0.00, 0.00,
1.90, 2.7 , 0.00,
2.20, 1.50, 2.7 ]
atoms = L1_2([[1,0,0],[0,1,0],[0,0,1]], size=(size,size,size),
element=("Cu", "Au"), periodic=(1,0,1), debug=0,
latticeconstant=3.95)
atoms.set_calculator(LennardJones(elements, epsilon, sigma, rCut, v0))
else:
elements = [29]
epsilon = [0.15]
sigma = [2.7]
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(size,size,size),
symbol="Cu", pbc=(1,0,1), debug=0,
latticeconstant=1.09*sigma[0]*1.41)
atoms.set_calculator(LennardJones(elements, epsilon, sigma, rCut, v0))
r = atoms.get_positions()
r.flat[:] += 0.06 * np.sin(np.arange(3*len(atoms)))
atoms.set_positions(r)
print " Running Verlet dynamics (%s)" % ("Cu",)
dyn = VelocityVerlet(atoms, 1*units.fs)
dyn.run(before)
etot1 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
for i in range(nsteps/10):
dyn.run(10)
#print atoms.get_potential_energy()/len(atoms), atoms.get_kinetic_energy()/len(atoms), (atoms.get_potential_energy() + atoms.get_kinetic_energy())/len(atoms)
etot2 = (atoms.get_potential_energy() + atoms.get_kinetic_energy())
ReportTest((" Energy conservation (%s)" % ("Cu",)), etot1, etot2, 2, silent=Silent)
print "Before: ", etot1, " now: ", etot2, " diff= ", (etot1-etot2)
epot = atoms.get_potential_energies()
stress = atoms.get_stresses()
print " Reporting energies and stresses"
e = []
s = []
j = 0
for i in range(0, len(atoms), 100):
e.append(epot[i])
s.append(stress[i,j])
j = (j + 1) % 6
print " e"+"Cu"+" =", repr(e)
print " s"+"Cu"+" =", repr(s)
end = time();
print " ++++ Test runtime of the LJ dynamicsTest was %d seconds ++++\n\n" %(end-start)
if 1:
sumstress = np.zeros(6, np.float)
for s in stress:
sumstress += s
totalstress = atoms.get_stress()
for i in range(6):
ReportTest("Sum of stresses (%d)" % (i,), sumstress[i]/len(atoms),
totalstress[i], abs(0.01*totalstress[i]))