#
# You should have received a copy of the GNU General Public License along with PyLaDa. If not, see
# <http://www.gnu.org/licenses/>.
###############################
from pylada.crystal.A2BX4 import b5
from pylada.enumeration import Enum
from spinel_check import checkme
# create spinel lattice and make it inverse.
lattice = Enum(b5())
for site in lattice.sites:
if "X" in site.type: continue
site.type = 'A' if 'B' in site.type else ('A', 'B')
lattice.find_space_group()
# look at inverse only.
def check_concentration(x, flavorbase, smith):
from pylada.enumeration import as_numpy
types = as_numpy(x, flavorbase)
result = 2*len(types[types == 1]) == len(types)
return result, None if result else False
result = [i for i, dummy, dummy, dummy in lattice.xn(2)]
result.append([i for i, dummy, dummy, dummy in lattice.xn(4)])
# creates file with result.
# with open("spinel_check.py", "w") as file:
def create_start(path, nall = 3, nrand = 5, nmax=100, density=10e0, input='input.py'):
""" Creates dictionary with input structures for Si/Ge.
:Parameters:
path : str
Path to output dictionary.
nall : int
All structure with ``nall`` (excluded) unit-cells are included in the final dictionary.
nrand : int
Structures between ``nall`` (included) and ``nrand`` (excluded) unit-cells are
also considered for inclusion in the final dictionary. However, only
``nmax`` are randomly chosen in the end.
nmax : int
Structures between ``nall`` (included) and ``nrand`` (excluded) unit-cells are
also considered for inclusion in the final dictionary. However, only
``nmax`` are randomly chosen in the end.
density : float
Kpoint density for escan calculations,
input : str
Path to input file containing escan functional.
Creates a job-dictionary with a number of structures sampled from an
exhaustive list of structures to evaluate using escan.
"""
from random import shuffle
from itertools import chain
from IPython.ipapi import get as get_ipy
from numpy.linalg import norm, inv
from pylada.enumeration import Enum
from pylada.crystal.binary import zinc_blende
from pylada.jobs import JobFolder
from pylada.escan import read_input, exec_input, ReducedKDensity
from pylada.crystal.gruber import Reduction
input = read_input(input)
kescan = exec_input(repr(input.escan).replace('Escan', 'KEscan')).functional
enum = Enum(zinc_blende())
enum.sites[0].type = 'Si', 'Ge'
enum.sites[1].type = 'Si', 'Ge'
enum.scale = 5.45
enum.find_space_group()
density = density * max([1e0/norm(u) for u in inv(enum.cell * enum.scale).T])
strs = [u for n in range(nall, nrand) for u in enum.xn(n)]
shuffle(strs)
strs = [enum.as_structure(*u) for u in strs[:nmax]]
alls = [structure for n in range(nall) for structure in enum.structures(n)]
jobs = JobFolder()
for i, structure in enumerate(chain(alls, strs)):
structure.name = str(i)
nSi = len([a.type for a in structure.atoms if a.type == 'Si'])
structure.scale = float(nSi) / float(n) * enum.scale + float(n - nSi) / float(n) * 5.69
jobfolder = jobs / structure.name
jobfolder.jobparams['structure'] = structure.copy()
jobfolder.structure.cell = Reduction()(jobfolder.structure.cell)
jobfolder.functional = kescan.copy()
jobfolder.functional.kpoints = ReducedKDensity(density, (0.5, 0.5, 0.5))
jobfolder.functional.reference = None
jobfolder.functional.fft_mesh = fftmesh(structure.cell)
jobfolder.functional.nbstates = int(len(structure.atoms) * 4 * 1.5+0.5)
ip = get_ipy()
ip.user_ns["current_jobfolder"] = jobfolder.root
ip.magic("savejobs " + path)
return