def from_atom_indices(cls,
atoms,
mask=None,
list=None,
force_fortran_indexing=True):
"""
Construct a new Table containing atomic indices from a list or mask
The new table will include 4 integer columns, for indices plus
shifts, and is suitable for passing to bfs_step,
construct_hysteretic_region, etc.
If force_fortran_indexing is True (the default), all atom indices
are converted to Fortran 1-based indexing.
"""
orig_fortran_indexing = get_fortran_indexing()
set_fortran_indexing(force_fortran_indexing)
try:
if mask is None and list is None:
raise ValueError('Either mask or list must be present.')
if list is not None and force_fortran_indexing and not orig_fortran_indexing:
# we were given 0-based atom indices, convert to 1-based indices
list = np.array(list) + 1
if mask is not None:
if len(mask) != len(atoms):
raise ValueError('size of mask must equal number of atoms')
mask = mask.astype(bool)
# use indexing style given by force_fortran_indexing
list = atoms.indices[mask]
self = cls(4, 0, 0, 0)
self.append(blank_rows=len(list))
self.int[:, :] = 0
if get_fortran_indexing():
first_column = 1
else:
first_column = 0
self.int[first_column, :] = list
finally:
set_fortran_indexing(orig_fortran_indexing)
self.atoms = weakref.ref(atoms)
return self
import argparse
import numpy as np
from ase.io.xyz import write_xyz
from quippy import AtomsReader
from quippy import set_fortran_indexing
set_fortran_indexing(False)
parser = argparse.ArgumentParser()
parser.add_argument("-r",
"--radius",
default=40.0,
type=float,
help="radius around cracktip to cutout (default 40\A)")
parser.add_argument("-i",
"--input",
default="crack_traj.xyz",
help="trajectory file to cut crack tip from.")
parser.add_argument("-o",
"--output",
default="cracktip_zone.xyz",
help="trajectory file to write cracktip region to.")
args = parser.parse_args()
def append(ats, rr, initial_crack, output_file='joined.xyz'):
num_images = len(ats)
for i, at in enumerate(ats):
print i + 1, '/', num_images, initial_crack
fixed_mask = (np.sqrt(
from matscipy.socketcalc import VaspClient, SocketCalculator
from simulate_crack import update_qm_region_context, fix_edges, set_qmmm_pot, pass_print_context,\
check_if_cracked_context, pass_trajectory_context
from quippy import Atoms, set_fortran_indexing
from quippy.io import AtomsWriter, AtomsReader
from quippy.lotf import LOTFDynamics, update_hysteretic_qm_region
from quippy.crack import get_strain, get_energy_release_rate,\
ConstantStrainRate, find_crack_tip_stress_field
from quippy.clusters import HYBRID_NO_MARK, HYBRID_ACTIVE_MARK
from quippy.potential import Potential, ForceMixingPotential
from quippy.system import verbosity_set_minimum, verbosity_to_str
set_fortran_indexing(False)
VERBOSITY = 3
verbosity_set_minimum(VERBOSITY)
print verbosity_to_str(VERBOSITY)
def log_pred_corr_errors(dynamics, logfile):
logline = '%s err %10.1f%12.6f%12.6f\n' % (dynamics.state_label,
dynamics.get_time()/units.fs,
dynamics.rms_force_error,
dynamics.max_force_error)
print logline
logfile.write(logline)
#lotf simulation parameters
extrapolate_steps = 5 # Number of steps for predictor-corrector
# interpolation and extrapolation
from ase.optimize import FIRE
from ase.optimize.precon import PreconFIRE, Exp
import argparse
from distutils import spawn
from imeall import app
from ForceMixerCarver import ForceMixingCarvingCalculator
from matscipy.socketcalc import VaspClient, SocketCalculator
from quippy import AtomsReader, AtomsWriter
from quippy import Potential, set_fortran_indexing
from imeall.calc_elast_dipole import find_h_atom
set_fortran_indexing(True)
class NEBAnalysis(object):
def __init__(self):
pass
def save_barriers(self, images, neb, prefix=""):
""" Saves the NEB results and plots energy barrier.
Arguments:
images ::
prefix ::
neb :: :class:ase:`NEB`
"""
if not os.path.exists('NEB_images'):
os.mkdir('NEB_images')
