def fcc211(symbol, size, a=None, vacuum=None, orthogonal=True):
"""FCC(211) surface.
Does not currently support special adsorption sites.
Currently only implemented for *orthogonal=True* with size specified
as (i, j, k), where i, j, and k are number of atoms in each direction.
i must be divisible by 3 to accommodate the step width.
"""
if not orthogonal:
raise NotImplementedError('Only implemented for orthogonal '
'unit cells.')
if size[0] % 3 != 0:
raise NotImplementedError('First dimension of size must be '
'divisible by 3.')
atoms = FaceCenteredCubic(symbol,
directions=[[1, -1, -1],
[0, 2, -2],
[2, 1, 1]],
miller=(None, None, (2, 1, 1)),
latticeconstant=a,
size=(1, 1, 1),
pbc=True)
z = (size[2] + 1) // 2
atoms = atoms.repeat((size[0] // 3, size[1], z))
if size[2] % 2: # Odd: remove bottom layer and shrink cell.
remove_list = [atom.index for atom in atoms
if atom.z < atoms[1].z]
del atoms[remove_list]
dz = atoms[0].z
atoms.translate((0., 0., -dz))
atoms.cell[2][2] -= dz
atoms.cell[2] = 0.0
atoms.pbc[2] = False
if vacuum:
atoms.center(vacuum, axis=2)
# Renumber systematically from top down.
orders = [(atom.index, round(atom.x, 3), round(atom.y, 3),
-round(atom.z, 3), atom.index) for atom in atoms]
orders.sort(key=itemgetter(3, 1, 2))
newatoms = atoms.copy()
for index, order in enumerate(orders):
newatoms[index].position = atoms[order[0]].position.copy()
# Add empty 'sites' dictionary for consistency with other functions
newatoms.info['adsorbate_info'] = {'sites': {}}
return newatoms
def fcc211(symbol, size, a=None, vacuum=None, orthogonal=True):
"""FCC(211) surface.
Does not currently support special adsorption sites.
Currently only implemented for *orthogonal=True* with size specified
as (i, j, k), where i, j, and k are number of atoms in each direction.
i must be divisible by 3 to accommodate the step width.
"""
if not orthogonal:
raise NotImplementedError('Only implemented for orthogonal '
'unit cells.')
if size[0] % 3 != 0:
raise NotImplementedError('First dimension of size must be '
'divisible by 3.')
atoms = FaceCenteredCubic(symbol,
directions=[[1, -1, -1],
[0, 2, -2],
[2, 1, 1]],
miller=(None, None, (2, 1, 1)),
latticeconstant=a,
size=(1, 1, 1),
pbc=True)
z = (size[2] + 1) // 2
atoms = atoms.repeat((size[0] // 3, size[1], z))
if size[2] % 2: # Odd: remove bottom layer and shrink cell.
remove_list = [atom.index for atom in atoms
if atom.z < atoms[1].z]
del atoms[remove_list]
dz = atoms[0].z
atoms.translate((0., 0., -dz))
atoms.cell[2][2] -= dz
atoms.cell[2] = 0.0
atoms.pbc[1] = False
if vacuum:
atoms.center(vacuum, axis=2)
# Renumber systematically from top down.
orders = [(atom.index, round(atom.x, 3), round(atom.y, 3),
-round(atom.z, 3), atom.index) for atom in atoms]
orders.sort(key=itemgetter(3, 1, 2))
newatoms = atoms.copy()
for index, order in enumerate(orders):
newatoms[index].position = atoms[order[0]].position.copy()
return newatoms
def test_center():
# flake8: noqa
"Test that atoms.center() works when adding vacuum ()"
import numpy as np
from math import pi, sqrt, cos
from ase import data
from ase.lattice.cubic import FaceCenteredCubic
def checkang(a, b, phi):
"Check the angle between two vectors."
cosphi = np.dot(a, b) / sqrt(np.dot(a, a) * np.dot(b, b))
assert np.abs(cosphi - cos(phi)) < 1e-10
symb = "Cu"
Z = data.atomic_numbers[symb]
a0 = data.reference_states[Z]['a']
# (100) oriented block
atoms = FaceCenteredCubic(size=(5, 5, 5), symbol="Cu", pbc=(1, 1, 0))
assert len(atoms) == 5 * 5 * 5 * 4
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(5 * a0 - c[2, 2]) < 1e-10
# Add vacuum in one direction
vac = 10.0
atoms.center(axis=2, vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[2, 2]) < 1e-10
# Add vacuum in all directions
vac = 4.0
atoms.center(vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 2)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[0, 0]) < 1e-10
assert np.abs(4.5 * a0 + 2 * vac - c[1, 1]) < 1e-10
assert np.abs(4.5 * a0 + 2 * vac - c[2, 2]) < 1e-10
# Now a general unit cell
atoms = FaceCenteredCubic(size=(5, 5, 5),
directions=[[1, 0, 0], [0, 1, 0], [1, 0, 1]],
symbol="Cu",
pbc=(1, 1, 0))
assert len(atoms) == 5 * 5 * 5 * 2
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2.5 * a0 - c[2, 2]) < 1e-10
# Add vacuum in one direction
vac = 10.0
atoms.center(axis=2, vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
# Recenter without specifying vacuum
atoms.center()
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
a2 = atoms.copy()
# Add vacuum in all directions
vac = 4.0
atoms.center(vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi / 2)
checkang(c[0], c[2], pi / 4)
checkang(c[1], c[2], pi / 2)
assert np.abs(4.5 * a0 + 2 * vac - c[1, 1]) < 1e-10
assert np.abs(2 * a0 + 2 * vac - c[2, 2]) < 1e-10
# One axis at the time:
for i in range(3):
a2.center(vacuum=vac, axis=i)
assert abs(atoms.positions - a2.positions).max() < 1e-12
assert abs(atoms.cell - a2.cell).max() < 1e-12
def get_structure(self, name, elements, a=None, c=None, l=None):
# Check number of elements
if name[:3] in ['fcc', 'hcp']:
if len(elements) != 1:
raise ValueError("Tuple of elements must be of length one")
if name[:3] in ['l12', 'l10'] or name[:2] == 'B2':
if len(elements) != 2:
raise ValueError("Tuple of elements must be of length two")
# Get lattice constants
if a is None:
if name[:2] == 'B2':
a = self.get_lattice_constant_a(name[:2], elements)
elif name[:3] in ['fcc', 'hcp', 'bcc', 'l12', 'l10']:
a = self.get_lattice_constant_a(name[:3], elements)
if c is None:
if name[:3] in ['hcp', 'l10']:
c = self.get_lattice_constant_c(name[:3], elements)
# Get size
if name in ['fcc', 'hcp', 'bcc', 'l12', 'l10', 'B2']:
size = self.properties[name + '_size']
elif name in ['fcc100', 'fcc111', 'hcp0001']:
size = self.properties[name + '_size'][:2] + (l, )
# Make structure
if name == 'fcc':
atoms = FaceCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'hcp':
atoms = HexagonalClosedPacked(symbol=elements[0],
size=size,
directions=[[2, -1, -1, 0],
[0, 1, -1, 0],
[0, 0, 0, 1]],
latticeconstant=(a, c))
elif name == 'bcc':
atoms = BodyCenteredCubic(symbol=elements[0],
size=size,
latticeconstant=a)
elif name == 'B2':
atoms = B2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l12':
atoms = L1_2(symbol=elements, size=size, latticeconstant=a)
elif name == 'l10':
atoms = L1_0(symbol=elements, size=size, latticeconstant=(a, c))
elif name == 'fcc100':
atoms = fcc100(symbol=elements[0], size=size, a=a, vacuum=10.0)
elif name == 'fcc111':
atoms = fcc111(symbol=elements[0],
size=size,
a=a,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp0001':
atoms = hcp0001(symbol=elements[0],
size=size,
a=a,
c=c,
vacuum=10.0,
orthogonal=True)
elif name == 'hcp1010A':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'hcp1010B':
raise ValueError("Structure '%s' not supported" % (name, ))
atoms = None
elif name == 'l12100':
n = (l + 1) / 2
atoms = L1_2(symbol=elements, size=(8, 8, n), latticeconstant=a)
atoms.set_pbc([True, True, False])
# Remove layers
atoms = atoms[atoms.get_positions()[:, 2] > 0.1 * a]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
elif name == 'l12111':
if l % 3 == 0:
n = l / 3
c = 0
else:
n = l / 3 + 1
c = 3 - l % 3
atoms = L1_2(
symbol=elements,
size=(8, 4, n),
#directions=[[1,-1,0],[1,0,-1],[1,1,1]], latticeconstant=a)
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]],
latticeconstant=a)
atoms.set_pbc([True, True, False])
# Wrap positions
scpos = atoms.get_scaled_positions()
scpos[scpos > (1.0 - 1e-12)] = 0.0
atoms.set_scaled_positions(scpos)
# Remove layers
if c > 0:
atoms = atoms[atoms.get_positions()[:, 2] > (c - 0.5) * a /
np.sqrt(3.0)]
# Set vacuum
atoms.center(axis=2, vacuum=10.0)
else:
raise ValueError("Structure '%s' not supported" % (name, ))
return atoms
if rank == 0:
print("#"*60)
print("GPAW benchmark: Copper Sheet")
print(" dimensions: x=%d, y=%d, z=%d" % (x, y, z))
print(" grid spacing: h=%f" % h)
print(" Brillouin-zone sampling: kpts=" + str(kpts))
print(" MPI task: %d out of %d" % (rank, size))
print(" using MICs: " + str(use_mic))
print("#"*60)
print("")
# setup the system
atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,-2], [1,1,1]],
size=(x,y,z), symbol='Cu', pbc=(1,1,0))
#add_vacuum(atoms, 10.0)
atoms.center(vacuum=6.0, axis=2)
calc = GPAW(h=h, nbands=-20, width=0.2,
kpts=kpts, xc='PBE',
maxiter=maxiter,
txt=txt, eigensolver=RMM_DIIS(niter=2),
parallel={'sl_auto': True},
mixer=Mixer(0.1, 5, 100),
)
atoms.set_calculator(calc)
# execute the run
try:
atoms.get_potential_energy()
except ConvergenceError:
pass
symb = "Cu" Z = data.atomic_numbers[symb] a0 = data.reference_states[Z]['a'] # (100) oriented block atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=(1,1,0)) assert len(atoms) == 5*5*5*4 c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(5 * a0 - c[2,2]) < 1e-10 # Add vacuum in one direction vac = 10.0 atoms.center(axis=2, vacuum=vac) c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 # Add vacuum in all directions vac = 4.0 atoms.center(vacuum=vac) c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(4.5 * a0 + 2* vac - c[0,0]) < 1e-10 assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10
from ase.io import write, read
from ase import units
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.verlet import VelocityVerlet
from ase.optimize import FIRE
from ase.md.langevin import Langevin
# Parameters for the Morse potential for Cu
D = 0.3429
r0 = 2.866
alpha = 1.3588
atoms = FaceCenteredCubic(latticeconstant=1.5, symbol='Cu', pbc=False, size=(3,3,3))
atoms.center(vacuum=100)
atoms.set_calculator(MorsePotential(D=D, alpha=alpha, r0=r0))
dyn = FIRE(atoms, trajectory='relax.traj')
dyn.run(fmax=0.01)
write('relax.xyz', read('relax.traj@:')) # uncomment this line for Task 2
open('langevin.log', 'w').close() # clean current log file
# dyn = VelocityVerlet(atoms, dt=1 * units.fs,
# trajectory='md.traj', logfile='md.log')
# dyn.run(1000)
from gpaw.mpi import size, rank
from gpaw import GPAW, Mixer, ConvergenceError
from gpaw.occupations import FermiDirac
from gpaw.eigensolvers.rmmdiis import RMMDIIS
from gpaw.test import equal
# no. of replicates in each dimension (increase to scale up the system)
x = 2
y = 2
z = 4
# setup the system
atoms = FaceCenteredCubic(directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]],
size=(x, y, z),
symbol='Cu',
pbc=(0, 0, 1))
atoms.center(vacuum=6.0, axis=0)
atoms.center(vacuum=6.0, axis=1)
# Simulation parameters
h = 0.22
kpts = (1, 1, 8)
txt = 'output_M_%i.txt' % size
maxiter = 15
# output benchmark parameters
if rank == 0:
print("#" * 60)
print("GPAW benchmark: Copper Filament")
print(" dimensions: x=%d, y=%d, z=%d" % (x, y, z))
print(" grid spacing: h=%f" % h)
print(" Brillouin-zone sampling: kpts=" + str(kpts))
radius = 15
size = [14, 10, 100]
# radius = 30
# size = [28, 20, 100] # 51500 atoms
a = FaceCenteredCubic('Au',
directions=[[1, 0, -1], [0, 1, 0], [1, 0, 1]],
size=size)
c = a.cell.diagonal() / 2
dir1 = [sqrt(2), 1, 0]
dir2 = [sqrt(2), -1, 0]
dir3 = [0, 1, 0]
dir1 = np.array(dir1) / np.linalg.norm(dir1)
dir2 = np.array(dir2) / np.linalg.norm(dir2)
dir3 = np.array(dir3) / np.linalg.norm(dir3)
r = a.get_positions() - c
m = np.abs(r.dot(dir1)) > radius
m = np.logical_or(m, np.abs(r.dot(dir2)) > radius)
m = np.logical_or(m, np.abs(r.dot(dir3)) > radius)
del a[m]
a.center()
a.set_pbc([False, False, True])
io.write('whisker.xyz', a)
io.write('whisker.data', a, format='lammps-data')
fast = False
#AsapThreads()
cpulayout = (1, 1, 2)
element = 'Pt'
size = (20, 20, 100)
master = world.rank == 0
if master:
atoms = FaceCenteredCubic(symbol=element,
size=size,
pbc=(True, True, False))
atoms.center(vacuum=10.0, axis=2)
atoms.set_momenta(np.zeros((len(atoms), 3)))
# Select an atom to get a kick
r = atoms.get_positions()
uc = atoms.get_cell()
x = r[:, 0] - 0.5 * uc[0, 0]
y = r[:, 1] - 0.5 * uc[1, 1]
z = r[:, 2]
zprime = z - 0.01 * (x * x + y * y)
n = np.argmax(zprime)
#a = atoms[n]
#dp = np.sqrt(2 * a.mass * 1000.0)
#a.momentum = np.array([0, 0, dp])
t = np.zeros(len(atoms), int)
t[n] = 1
atoms.set_tags(t)
from MorseCalculator import MorsePotential
from ase.io import write, read
from ase import units
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.verlet import VelocityVerlet
# Parameters for the Morse potential for Cu
D = 0.3429
r0 = 2.866
alpha = 1.3588
atoms = FaceCenteredCubic(latticeconstant=1.5,
symbol='Cu',
pbc=False,
size=(3, 3, 3))
atoms.center(vacuum=100) #size of box
atoms.set_calculator(MorsePotential(D=D, alpha=alpha, r0=r0))
# write('relax.xyz', read('relax.traj@:')) # uncomment this line for Task 2
open('md.log', 'w').close() # clean current log file
dyn = VelocityVerlet(atoms,
dt=1 * units.fs,
trajectory='md.traj',
logfile='md.log')
dyn.run(1000)
write('md.xyz', read('md.traj@:'))
# write('langevin.xyz', read('langevin.traj@:')) # uncomment this line for Task 3
symb = "Cu" Z = data.atomic_numbers[symb] a0 = data.reference_states[Z]['a'] # (100) oriented block atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=(1,1,0)) assert len(atoms) == 5*5*5*4 c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(5 * a0 - c[2,2]) < 1e-10 # Add vacuum in one direction vac = 10.0 atoms.center(axis=2, vacuum=vac) c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10 # Add vacuum in all directions vac = 4.0 atoms.center(vacuum=vac) c = atoms.get_cell() checkang(c[0], c[1], pi/2) checkang(c[0], c[2], pi/2) checkang(c[1], c[2], pi/2) assert np.abs(4.5 * a0 + 2* vac - c[0,0]) < 1e-10 assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10
def main(element, T_up, T_low, T_expect, bulkmodulus, makepot):
def set_temp_fric(dyn, atoms):
z = atoms.get_positions()[:,2]
zmax = atoms.get_cell()[2,2]
zmin = 0
T = T_low + (T_up - T_low) * (z - zmin) / (zmax - zmin)
dyn.set_temperature(T * units.kB)
rnd = world.sum(random.randint(0,2**32)) # Insures the same number on all nodes.
prefix = "melt-%s-%s" % (element, hex(rnd)[2:])
if master:
print "Using output directory", prefix
os.mkdir(prefix)
else:
while not os.path.exists(prefix):
time.sleep(1)
if master:
atoms = FaceCenteredCubic(symbol=element, size=size, pbc=(True, True, False))
atoms.center(vacuum=10.0, axis=2)
else:
atoms = None
atoms = MakeParallelAtoms(atoms, cpulayout1)
print world.rank, '-', len(atoms), atoms.get_number_of_atoms()
atoms.set_calculator(makepot())
#view(atoms)
dyn = Langevin(atoms, 5*units.fs, 0.0, friction)
logger = MDLogger(dyn, atoms, prefix+'/Melt-phase1.log', stress=True, peratom=True)
dyn.attach(logger, interval=100)
set_temp_fric(dyn, atoms)
unstress = Inhomogeneous_NPTBerendsen(atoms, 50*units.fs, 0, taup=500*units.fs,
compressibility=1/bulkmodulus)
dyn.attach(unstress.scale_positions_and_cell, interval=10)
#traj = PickleTrajectory("melting-phase1.traj", "w", atoms)
fn1 = prefix + "/Melt-phase1.bundle"
if master:
print "Opening file", fn1
traj = BundleTrajectory(fn1, "w", atoms, split=True)
dyn.attach(traj, interval=500)
therm = Thermometer(atoms, prefix+"/TempProfile-phase1.dat")
dyn.attach(therm.update, interval=500)
for i in range(steps1 / 100):
dyn.run(100)
set_temp_fric(dyn, atoms)
if master:
print "Closing file", fn1
traj.close()
del traj, atoms
# Reread the bundle
atoms = BundleTrajectory(fn1).get_atoms(-1, cpulayout2)
atoms.set_calculator(makepot())
dyn = VelocityVerlet(atoms, 5*units.fs)
logger = MDLogger(dyn, atoms, prefix+'/PtMelt-phase2.log', stress=True, peratom=True)
dyn.attach(logger, interval=1000)
unstress = Inhomogeneous_NPTBerendsen(atoms, 50*units.fs, 0,
taup=5000*units.fs,
compressibility=1/bulkmodulus)
dyn.attach(unstress.scale_positions_and_cell, interval=10)
fn2 = prefix + "/Melt-phase2.bundle"
if master:
print "Opening file", fn2
traj = BundleTrajectory(fn2, "w", atoms)
dyn.attach(traj, interval=steps2/100)
therm = Thermometer(atoms, prefix+"/TempProfile-phase2.dat")
dyn.attach(therm.update, interval=steps2/10)
dyn.run(steps2 - takedata)
therm2 = AveragingThermometer(atoms)
dyn.attach(therm2.update, interval=100)
dyn.run(takedata) # Run the last part
T = therm2.get_temp()
if master:
print "Melting temperature:", T
ReportTest("Melting temperature", T, T_expect, 3)
if cleanup:
world.barrier()
# Cleanup may fail due to the directory not being updated from
# writes on the other nodes. Wait for NFS file system.
time.sleep(60)
if master:
shutil.rmtree(prefix)
world.barrier()
ReportTest.Summary()
