def _get_images_by_linear_interp(self, nimages, ep0, ep1):
logger = get_logger(__name__)
sort_tol = self.get("sort_tol", 0.0)
try:
images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=sort_tol)
except Exception as e:
if "Unable to reliably match structures " in str(e):
logger.warn("Auto sorting is turned off because it is unable to match the "
"end-point structures!")
images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=0)
else:
raise e
return images
def _get_images_by_linear_interp(self, nimages, ep0, ep1):
logger = get_logger(__name__)
sort_tol = self.get("sort_tol", 0.0)
try:
images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=sort_tol)
except Exception as e:
if "Unable to reliably match structures " in str(e):
logger.warning("Auto sorting is turned off because it is unable to match the "
"end-point structures!")
images = ep0.interpolate(ep1, nimages=nimages + 1, autosort_tol=0)
else:
raise e
return images
# coding: utf-8
from __future__ import absolute_import, division, print_function, unicode_literals
from tqdm import tqdm
from matgendb.util import get_database
from pymatgen import Composition
from atomate.vasp.builders.base import AbstractBuilder
from atomate.utils.utils import get_logger
logger = get_logger(__name__)
__author__ = 'Anubhav Jain <*****@*****.**>'
class FileMaterialsBuilder(AbstractBuilder):
def __init__(self, materials_write, data_file, delimiter=",", header_lines=0):
"""
Updates the database using a data file. Format of file must be:
<material_id or formula>, <property>, <value>
Comment lines should *start* with '#'.
Args:
materials_write: mongodb collection for materials (write access needed)
data_file (str): path to data file
delimiter (str): delimiter for file parsing
header_lines (int): number of header lines to skip in data file
add_tags,
add_additional_fields_to_taskdocs,
add_wf_metadata,
add_common_powerups,
)
from atomate.vasp.workflows.base.core import get_wf
from atomate.vasp.firetasks.parse_outputs import (
MagneticDeformationToDB,
MagneticOrderingsToDB,
)
from pymatgen.alchemy.materials import TransformedStructure
from atomate.utils.utils import get_logger
logger = get_logger(__name__)
from atomate.vasp.config import VASP_CMD, DB_FILE, ADD_WF_METADATA
from atomate.vasp.workflows.presets.scan import wf_scan_opt
from uuid import uuid4
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.core import Lattice, Structure
from pymatgen.analysis.magnetism.analyzer import (
CollinearMagneticStructureAnalyzer,
MagneticStructureEnumerator,
)
__author__ = "Matthew Horton"
__maintainer__ = "Matthew Horton"
__email__ = "*****@*****.**"