def makecrack_main(params, stem):
"""Given a CrackParams object `param`, construct and return a new crack slab Atoms object."""
xmlfilename = stem+'.xml'
print_title('Initialisation')
verbosity_push(params.io_verbosity)
params.print_()
print("Initialising classical potential with args " + params.classical_args.strip() +
" from file " + xmlfilename)
classicalpot = Potential(params.classical_args, param_filename=xmlfilename)
classicalpot.print_()
mpi_glob = MPI_context()
crack_slab, width, height, E, v, v2, bulk = crack_make_slab(params, classicalpot)
if params.crack_free_surfaces:
depth = crack_slab.pos[3,:].max() - crack_slab.pos[3,:].min()
else:
depth = crack_slab.lattice[3,3]
# Save bulk cube (used for qm_rescale_r parameter in crack code)
if params.qm_args.startswith('TB'):
bigger_bulk = supercell(bulk, 2, 2, 2)
bulk = bigger_bulk
bulk.write(stem+'_bulk.xyz')
crack_slab.write(stem+'_slab.xyz')
crack_slab.params['OrigWidth'] = width
crack_slab.params['OrigHeight'] = height
crack_slab.params['OrigDepth'] = depth
crack_slab.params['YoungsModulus'] = E
crack_slab.params['PoissonRatio_yx'] = v
crack_slab.params['PoissonRatio_yz'] = v2
# Open surfaces, remain periodic in z direction (normal to plane)
# and optionally also in x direction if crack_double_ended is true
if not params.crack_double_ended:
crack_slab.lattice[1,1] = crack_slab.lattice[1,1] + params.crack_vacuum_size
crack_slab.lattice[2,2] = crack_slab.lattice[2,2] + params.crack_vacuum_size
crack_slab.set_lattice(crack_slab.lattice, False)
# 3D crack with free surfaces at z = +/- depth/2
if params.crack_free_surfaces:
crack_slab.pos[3,:] -= crack_slab.pos[3,:].mean() # center on z=0
crack_slab.lattice[3,3] = crack_slab.lattice[3,3] + params.crack_vacuum_size
crack_slab.set_lattice(crack_slab.lattice, False)
# Map atoms into cell AFTER changing to the new lattice
crack_slab.map_into_cell()
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
assert abs((maxy-miny) - height) < 1e-5 # be sure that remapping didn't change height of slab
# Add various properties to crack_slab
crack_slab.add_property('hybrid', 0)
crack_slab.add_property('hybrid_mark', HYBRID_NO_MARK)
crack_slab.add_property('changed_nn', 0)
crack_slab.add_property('move_mask', 0)
crack_slab.add_property('nn', 0)
crack_slab.add_property('old_nn', 0)
crack_slab.add_property('md_old_changed_nn', 0)
crack_slab.add_property('edge_mask', 0)
crack_slab.add_property('crack_surface', False)
crack_slab.add_property('crack_front', False)
if params.crack_fix_dipoles:
crack_slab.add_property('fixdip', False)
print_title('Fixing Atoms')
# Fix top and bottom edges - anything within crack_edge_fix_tol of ymax or ymin is fixed
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
crack_slab.move_mask[:] = 1
crack_slab.move_mask[(abs(crack_slab.pos[2,:]-maxy) < params.crack_edge_fix_tol) |
(abs(crack_slab.pos[2,:]-miny) < params.crack_edge_fix_tol)] = 0
if params.crack_fix_sides:
maxx, minx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.move_mask[(abs(crack_slab.pos[1,:]-maxx) < params.crack_edge_fix_tol) |
(abs(crack_slab.pos[1,:]-minx) < params.crack_edge_fix_tol)] = 0
print('%d atoms. %d fixed atoms' % (crack_slab.n, crack_slab.n - crack_slab.move_mask.sum()))
print_title('Setting edge mask')
crack_slab.edge_mask[:] = 0
minx, maxx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[1,:]-minx) < params.selection_edge_tol) |
(abs(crack_slab.pos[1,:]-maxx) < params.selection_edge_tol)] = 1
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[2,:]-miny) < params.selection_edge_tol) |
(abs(crack_slab.pos[2,:]-maxy) < params.selection_edge_tol)] = 1
if params.crack_free_surfaces:
# Open surfaces at +/- z
minz, maxz = crack_slab.pos[3,:].min(), crack_slab.pos[3,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[3,:]-minz) < params.selection_edge_tol) |
(abs(crack_slab.pos[3,:]-maxz) < params.selection_edge_tol)] = 1
if params.crack_fix_dipoles:
print_title('Fixing dipoles')
crack_slab.fixdip[(abs(crack_slab.pos[2,:]-maxy) < params.crack_fix_dipoles_tol) |
(abs(crack_slab.pos[2,:]-miny) < params.crack_fix_dipoles_tol)] = 1
if params.crack_fix_sides:
maxx, minx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.fixdip[(abs(crack_slab.pos[1,:]-maxx) < params.crack_fix_dipoles_tol) |
(abs(crack_slab.pos[1,:]-minx) < params.crack_fix_dipoles_tol)] = 1
if params.crack_curved_front:
crack_make_seed_curved_front(crack_slab, params)
else:
crack_make_seed(crack_slab, params)
if params.crack_apply_initial_load:
crack_calc_load_field(crack_slab, params, classicalpot,
params.crack_loading, overwrite_pos=True,
mpi=mpi_glob)
crack_slab.write('dump.xyz')
crack_update_connect(crack_slab, params)
if not params.simulation_classical:
if (params.selection_method.strip() == 'crack_front' or
params.crack_tip_method.strip() == 'local_energy'):
classicalpot.calc(crack_slab, local_energy=True)
crack_setup_marks(crack_slab, params)
crack_update_selection(crack_slab, params)
if params.any_per_atom_tau():
# Set up per_atom_tau property for ramped Langevin thermostat:
#
# tau
# ^
# |\ /| |\ /| max_tau
# | \ / | | \ / |
# | \ / | constant E | \ / |
# | \ / | (tau = 0) | \ / |
# | \/ | | \/ |
# +----------+---------------------+----------+---> x
# -w/2 -w/2+r w/2-r w/2
w_by_2 = crack_slab.OrigWidth/2.
ramp_len = params.crack_thermostat_ramp_length
max_tau = params.crack_thermostat_ramp_max_tau
print 'Adding thermostat ramp with length', ramp_len, 'max_tau', max_tau
@np.vectorize
def tau(x):
if x < -w_by_2 + ramp_len/2:
q = (x+w_by_2)/(ramp_len/2.)
return max_tau*(1.- q)
elif (x > -w_by_2 + ramp_len/2 and
x < -w_by_2 + ramp_len):
q = (x+w_by_2-ramp_len/2.)/(ramp_len/2.)
return max_tau*q
elif (x > -w_by_2 + ramp_len and
x < w_by_2 - ramp_len):
return 0.
elif (x > w_by_2 - ramp_len and
x < w_by_2 - ramp_len/2):
q = (x-w_by_2+ramp_len)/(ramp_len/2.)
return max_tau*(1.- q)
else:
q = (x-w_by_2+ramp_len/2.)/(ramp_len/2.)
return max_tau*q
crack_slab.add_property('per_atom_tau', tau(crack_slab.pos[1,:]))
return crack_slab
def crack_strain_energy_release_rate(at, bulk=None, f_min=.8, f_max=.9, stem=None, avg_pos=False):
"""
Compute strain energy release rate G from elastic potential energy in a strip
"""
print 'Analytical effective elastic modulus E\' = ', at.YoungsModulus/(1-at.PoissonRatio_yx**2), 'GPa'
print 'Analytical energy release rate G = ', crack_measure_g(at, at.YoungsModulus, at.PoissonRatio_yx, at.OrigHeight), 'J/m^2'
if bulk is None:
if stem is None: raise ValueError('Either "bulk" or "stem" must be present')
bulk = Atoms(stem+'_bulk.xyz')
if not hasattr(at, 'local_energy') or not hasattr(bulk, 'energy'):
if stem is None: raise ValueError('local_energy property not found in Atoms and "stem" is missing')
xmlfile = stem+'.xml'
params = CrackParams(xmlfile)
pot = Potential(params.classical_args, param_filename=stem+'.xml')
pot.print_()
if not hasattr(at, 'local_energy'):
if avg_pos:
tmp_pos = at.pos.copy()
at.pos[...] = at.avgpos
at.set_cutoff(pot.cutoff()+1.)
at.calc_connect()
pot.calc(at, args_str="local_energy")
if avg_pos:
at.pos[...] = tmp_pos
if not hasattr(bulk, 'energy'):
bulk.set_cutoff(pot.cutoff()+1.)
bulk.calc_connect()
pot.calc(bulk, args_str='energy')
h = at.pos[2,:].max() - at.pos[2,:].min()
h0 = at.OrigHeight
strain = (h - h0)/h0
print 'Applied strain', strain
x_min = f_min*at.OrigWidth - at.OrigWidth/2.
x_max = f_max*at.OrigWidth - at.OrigWidth/2.
strip = np.logical_and(at.move_mask == 1, np.logical_and(at.pos[1,:] > x_min, at.pos[1,:] < x_max))
at.add_property('strip', strip, overwrite=True)
strip_depth = at.lattice[3,3]
strip_width = at.pos[1,strip].max() - at.pos[1,strip].min()
strip_height = at.pos[2,strip].max() - at.pos[2,strip].min()
strip_volume = strip_width*strip_height*strip_depth
print 'Strip contains', strip.sum(), 'atoms', 'width', strip_width, 'height', strip_height, 'volume', strip_volume
strain_energy_density = (at.local_energy[strip].sum() - bulk.energy/bulk.n*strip.sum())/strip_volume
print 'Strain energy density in strip', strain_energy_density, 'eV/A**3'
E_effective = 2*strain_energy_density/strain**2*GPA
print 'Effective elastic modulus E =', E_effective, 'GPa'
G_effective = strain_energy_density*strip_height*J_PER_M2
print 'Effective energy release rate G =', G_effective, 'J/m^2'
return G_effective
def molecular_dynamics(system,
potential,
potential_filename=None,
temperature=300,
total_steps=1100000,
timestep=1.0,
connect_interval=200,
write_interval=20000,
equilibration_steps=100000,
out_of_plane=None,
random_seed=None):
"""
Run very simple molecular dynamics to generate some configurations. Writes
configurations out as xyz and CASTEP files.
"""
info("Inside MD.")
if random_seed is None:
random_seed = random.SystemRandom().randint(0, 2**63)
quippy.system.system_set_random_seeds(random_seed)
info("Quippy Random Seed {0}.".format(random_seed))
system = Atoms(system)
# Can take Potential objects, or just use a string
if not isinstance(potential, Potential):
if potential_filename:
potential = Potential(potential, param_filename=potential_filename)
else:
potential = Potential(potential)
system.set_calculator(potential)
dynamical_system = DynamicalSystem(system)
with Capturing(debug_on_exit=True):
dynamical_system.rescale_velo(temperature)
if out_of_plane is not None:
# Stop things moving vertically in the cell
dynamical_system.atoms.velo[3, :] = 0
base_dir = os.getcwd()
run_path = '{0}_{1:g}/'.format(system.info['name'], temperature)
info("Putting files in {0}.".format(run_path))
os.mkdir(run_path)
os.chdir(run_path)
trajectory = 'traj_{0}_{1:g}.xyz'.format(system.info['name'], temperature)
out = AtomsWriter(trajectory)
dynamical_system.atoms.set_cutoff(potential.cutoff() + 2.0)
dynamical_system.atoms.calc_connect()
potential.calc(dynamical_system.atoms,
force=True,
energy=True,
virial=True)
structure_count = 0
# Basic NVE molecular dynamics
for step_number in range(1, total_steps + 1):
dynamical_system.advance_verlet1(timestep,
virial=dynamical_system.atoms.virial)
potential.calc(dynamical_system.atoms,
force=True,
energy=True,
virial=True)
dynamical_system.advance_verlet2(timestep,
f=dynamical_system.atoms.force,
virial=dynamical_system.atoms.virial)
# Maintenance of the system
if not step_number % connect_interval:
debug("Connect at step {0}".format(step_number))
dynamical_system.atoms.calc_connect()
if step_number < equilibration_steps:
with Capturing(debug_on_exit=True):
dynamical_system.rescale_velo(temperature)
if not step_number % write_interval:
debug("Status at step {0}".format(step_number))
# Print goes to captured stdout
with Capturing(debug_on_exit=True):
dynamical_system.print_status(
epot=dynamical_system.atoms.energy)
dynamical_system.rescale_velo(temperature)
if step_number > equilibration_steps:
debug("Write at step {0}".format(step_number))
out.write(dynamical_system.atoms)
sp_path = '{0:03d}'.format(structure_count)
write_filename = '{0}_{1:g}.{2:03d}'.format(
system.info['name'], temperature, structure_count)
os.mkdir(sp_path)
os.chdir(sp_path)
castep_write(dynamical_system.atoms, filename=write_filename)
espresso_write(dynamical_system.atoms, prefix=write_filename)
write_extxyz("{0}.xyz".format(write_filename),
dynamical_system.atoms)
info("Wrote a configuration {0}.".format(write_filename))
os.chdir('..')
structure_count += 1
out.close()
os.chdir(base_dir)
info("MD Done.")
# setup clusters to be calculated
d = diamond(5.44, 14)
at = supercell(d, 2, 2, 2)
at.rattle(0.05)
at.calc_connect()
clusters = list(
iter_atom_centered_clusters(at, buffer_hops=4, randomise_buffer=False))
pot = Potential('IP SW', param_filename='params.xml')
for i, c in enumerate(clusters):
client_id, nstep = i % N_JOBS, i // N_JOBS
data = pack_atoms_to_reftraj_str(c, nstep)
cluster_map[(client_id, nstep)] = (c, i)
input_qs[client_id].put(data)
pot.calc(c, args_str='energy force virial')
t_clus = time.time()
# write initial input file for each client
for client_id, input_q in enumerate(input_qs):
data = input_q.get()
c, i = cluster_map[(client_id, 0)]
c.write('atoms.%d.xyz' % client_id, real_format=MSG_FLOAT_FORMAT)
scp = subprocess.Popen(
['scp', 'atoms.%d.xyz' % client_id, remote_host + ':'])
scp.wait()
t_input = time.time()
for param_file in param_files:
def quippy_client(ip, port, client_id, maxsteps):
pot = Potential('IP SW')
args_str = 'force energy virial'
print 'Starting client with ID %d maxsteps %d' % (client_id, maxsteps)
for step in range(maxsteps):
# open connection to server
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.connect((ip, port))
try:
# say hello and ask server for some Atoms (status 'A')
# identify ourselves with an ID number, formatted as an 8-byte ascii string
id_str = ('A%7d' % client_id).encode('ascii')
totalsent = 0
while totalsent < MSG_LEN_SIZE:
sent = sock.send(id_str[totalsent:])
if sent == 0:
raise RuntimeError('socket connection broken while sending client ID')
totalsent += sent
# now receive the length of the data, formatted as an 8-byte ascii string
data_length = ''
while len(data_length) < MSG_LEN_SIZE:
chunk = sock.recv(MSG_LEN_SIZE - len(data_length))
if not chunk:
raise RuntimeError('socket connection broken while reading length')
data_length += chunk
data_length = int(data_length)
# now receive the data itself
data = ''
while len(data) < data_length:
chunk = sock.recv(data_length - len(data))
if not chunk:
raise RuntimeError('socket connection broken while reading data')
data += chunk
# and finally receive the end marker
marker = ''
while len(marker) < MSG_END_MARKER_SIZE:
chunk = sock.recv(MSG_END_MARKER_SIZE - len(marker))
if not chunk:
raise RuntimeError('socket connection broken while reading end marker')
marker += chunk
assert marker == MSG_END_MARKER
finally:
sock.close()
# construct Atoms object from data string in REFTRAJ format
at = unpack_reftraj_str_to_atoms(data)
# do the calculation - this will take a long time in real use-case
pot.calc(at, args_str=args_str)
print 'client %d calculation on %d atoms complete' % (client_id, len(at))
# format the results into a string, cf. vasp_driver REJTRAJ_OUTPUT format
data = pack_results_to_reftraj_output_str(at)
# open a new connection to the server to send back the results
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.connect((ip, port))
try:
# say hello and tell server we've got some results (status 'R')
# identify ourselves with an ID number, formatted as an 8-byte ascii string
id_str = ('R%7d' % client_id).encode('ascii')
totalsent = 0
while totalsent < MSG_LEN_SIZE:
sent = sock.send(id_str[totalsent:])
if sent == 0:
raise RuntimeError('socket connection broken while sending client ID')
totalsent += sent
# send back results of the calculation
totalsent = 0
while totalsent < len(data):
sent = sock.send(data[totalsent:])
if sent == 0:
raise RuntimeError('socket connection broken while sending results')
totalsent += sent
# wait to receive the end marker
marker = ''
while len(marker) < MSG_END_MARKER_SIZE:
chunk = sock.recv(MSG_END_MARKER_SIZE - len(marker))
if not chunk:
raise RuntimeError('socket connection broken while reading end marker')
marker += chunk
assert marker == MSG_END_MARKER
finally:
sock.close()
w_epsilon=10000.0, w_epsilon_factor=10000.0,
t=TEMPERATURE)
dynamical_system.add_thermostat(type=THERMOSTAT_ALL_PURPOSE, t=TEMPERATURE, tau=100.0)
dynamical_system.rescale_velo(TEMPERATURE)
total_steps = 1100000
timestep = 0.1 # fs
connect_interval = 200
write_interval = 20000
equilibration_steps = 100000
trajectory = 'traj_{}_{}.xyz'.format(lattice.func_name, TEMPERATURE)
out = AtomsWriter(trajectory)
dynamical_system.atoms.calc_connect()
fs_potential.calc(dynamical_system.atoms, force=True, energy=True, virial=True)
# Basic NVE molecular dynamics
for step_number in range(1, total_steps+1):
dynamical_system.advance_verlet1(timestep,
virial=dynamical_system.atoms.virial)
fs_potential.calc(dynamical_system.atoms, force=True,
energy=True, virial=True)
dynamical_system.advance_verlet2(timestep, f=dynamical_system.atoms.force,
virial=dynamical_system.atoms.virial)
# Maintenance of the system
if not step_number % connect_interval:
dynamical_system.atoms.calc_connect()
if step_number < equilibration_steps:
dynamical_system.rescale_velo(TEMPERATURE)
