# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os
from httk.core import citation
from httk.core.basic import is_sequence
citation.add_ext_citation('Atomic Simulation Environment (ASE)',
"S. R. Bahn, K. W. Jacobsen")
import httk.atomistic.data
from httk.core.httkobject import HttkPlugin, HttkPluginWrapper
from httk.atomistic import Cell
from httk.atomistic.spacegrouputils import get_symops_strs, spacegroup_get_number_and_setting
from httk import config
from httk.atomistic import Structure, UnitcellSites
import httk.iface
from httk.iface.ase_if import *
from httk.external.subimport import submodule_import_external
ase_major_version = None
ase_minor_version = None
try:
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
pyspglib external module
"""
import os, sys
from httk.core import citation
citation.add_ext_citation('spglib / pyspglib', "(Author list to be added)")
from httk import config
from httk.external.command import Command
from httk.external.subimport import submodule_import_external
import httk
try:
pyspglib_path = config.get('paths', 'pyspglib')
except Exception:
pyspglib_path = None
try:
spglib_path = config.get('paths', 'spglib')
except Exception:
spglib_path = None
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from httk.core import citation
citation.add_ext_citation('Platon', "A. L. Spek, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.")
import os, sys, tempfile
from httk import config
from httk.external.command import Command
import httk
if sys.version_info[0] == 3:
from io import StringIO
else:
from StringIO import StringIO
platon_path = None
def ensure_has_platon():
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
import sys, os, tempfile
from httk.core import citation, IoAdapterString
citation.add_ext_citation(
'isotropy',
"Harold T. Stokes, Dorian M. Hatch, and Branton J. Campbell, Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84606, USA"
)
from httk.core.basic import int_to_anonymous_symbol
from httk import config
from httk.external.command import Command
import httk.httkio
import httk.iface
from httk.atomistic.atomisticio.structure_cif_io import cif_to_struct
from httk.atomistic.data.periodictable import atomic_symbol, atomic_number
isotropy_path = None
def ensure_has_isotropy():
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
from httk.core import citation
citation.add_ext_citation(
'Jmol',
"An open-source Java viewer for chemical structures in 3D. http://www.jmol.org/"
)
import os, time, threading, subprocess, signal, sys, glob
import httk
from httk.iface.jmol_if import *
import distutils.spawn
from httk import config
from httk.core.basic import create_tmpdir, destroy_tmpdir, micro_pyawk
from httk.external.command import Command, find_executable
jmol_path = None
jmol_version = None
jmol_version_date = None
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from httk.core import citation
citation.add_ext_citation('aflow', "(Author list to be added)")
from httk import config
from httk.external.command import Command
import httk
try:
aflow_path = config.get('paths', 'aflow')
except Exception:
aflow_path = None
raise Exception("httk.external.aflow imported with no aflow path set in httk.cfg")
def aflow(ioa_in, args, timeout=30):
ioa_in = httk.IoAdapterString.use(ioa_in)
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os
from httk.core import citation
from httk.core.basic import is_sequence
citation.add_ext_citation(
"Pymatgen",
"Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher, \
Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A. Persson, Gerbrand Ceder. \
Python Materials Genomics (pymatgen) : A Robust, Open-Source Python Library for Materials Analysis. \
Computational Materials Science, 2013, 68, 314-319. \
doi:10.1016/j.commatsci.2012.10.028; and others")
import httk.atomistic.data
from httk.core.httkobject import HttkPlugin, HttkPluginWrapper
from httk import config
from httk.atomistic import Structure, UnitcellSites
import httk.iface
from httk.external.subimport import submodule_import_external
try:
pymatgen_path = config.get('paths', 'pymatgen')
except Exception:
pymatgen_path = None
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os, distutils, glob
from httk.core import citation, IoAdapterString
from httk.atomistic.atomisticio.structure_cif_io import struct_to_cif
from httk.atomistic import Structure
citation.add_ext_citation('cif2cell', "Torbjörn Björkman")
from httk import config
from httk.external.command import Command, find_executable
import httk
import httk.iface
cif2cell_path = None
def ensure_has_cif2cell():
if cif2cell_path is None or cif2cell_path == "" or not os.path.exists(
cif2cell_path):
raise ImportError(
"httk.external.cif2cell_ext imported with no access to cif2cell binary"
)