def test_6(self):
from phenum.phonons import enum_sys
from numpy import array
groupfile = None
concs = [3, 1, 2]
a_cons = [0.0, 0.5, 0.25]
num_wanted = 6
HNF = array([1, 0, 1, 0, 0, 6])
params = {
'bulk':
True,
'nspecies':
3,
'concs': [[1.0, 6.0, 12.0, 0.0], [1.0, 9.0, 12.0, 0.5],
[1.0, 12.0, 12.0, 0.25]],
'basis_vecs': [[0.0, 0.0, 0.0]],
'sizes': [6, 6],
'lat_vecs': [[0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5]],
'arrows':
True,
'is_crestricted':
True
}
out = _read_output("enum_sys.out.6")
self.assertEqual(
enum_sys(groupfile, concs, a_cons, num_wanted, HNF, params, True),
out)
def test_5(self):
from phenum.phonons import enum_sys
from numpy import array
groupfile = "tests/phonons/test_group.5"
concs = [4,4]
a_cons = [0,0]
num_wanted = 10
HNF = array([1,0,2,0,0,4])
params = {'bulk': True, 'nspecies': 2, 'concs': [], 'basis_vecs': [[0.0, 0.0, 0.0]], 'sizes': [1, 11], 'lat_vecs': [[0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5]], 'arrows': False, 'is_crestricted': False}
out = [[[-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2], [-1, 2]], [[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 2], [-1, 2]], [[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 2]], [[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2], [-1, 2], [-1, 1]], [[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 1], [-1, 2], [-1, 2]], [[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 1], [-1, 2]], [[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 2], [-1, 1]], [[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2], [-1, 2], [-1, 1], [-1, 1]], [[-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 1], [-1, 2]], [[-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 1]]]
self.assertEqual(enum_sys(groupfile,concs,a_cons,num_wanted,HNF,params,True),out)
def test_5(self):
from phenum.phonons import enum_sys
from numpy import array
groupfile = "tests/phonons/test_group.5"
concs = [4, 4]
a_cons = [0, 0]
num_wanted = 10
HNF = array([1, 0, 2, 0, 0, 4])
params = {
'bulk': True,
'nspecies': 2,
'concs': [],
'basis_vecs': [[0.0, 0.0, 0.0]],
'sizes': [1, 11],
'lat_vecs': [[0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5]],
'arrows': False,
'is_crestricted': False
}
out = [[[-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2],
[-1, 2]],
[[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 2],
[-1, 2]],
[[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2],
[-1, 2]],
[[-1, 1], [-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2], [-1, 2],
[-1, 1]],
[[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 1], [-1, 2],
[-1, 2]],
[[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 1],
[-1, 2]],
[[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2], [-1, 2],
[-1, 1]],
[[-1, 1], [-1, 1], [-1, 2], [-1, 2], [-1, 2], [-1, 2], [-1, 1],
[-1, 1]],
[[-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 1],
[-1, 2]],
[[-1, 1], [-1, 2], [-1, 1], [-1, 2], [-1, 2], [-1, 1], [-1, 2],
[-1, 1]]]
self.assertEqual(
enum_sys(groupfile, concs, a_cons, num_wanted, HNF, params, True),
out)
def test_3(self):
from numpy import array
from phenum.phonons import enum_sys
groupfile = "tests/phonons/test_group.3"
concs = [4, 3]
a_cons = [0, 0]
num_wanted = 4
HNF = array([1, 0, 1, 1, 2, 7])
params = {
'bulk': True,
'nspecies': 2,
'concs': [],
'basis_vecs': [[0.0, 0.0, 0.0]],
'sizes': [1, 11],
'lat_vecs': [[0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5]],
'arrows': False,
'is_crestricted': False
}
out = _read_output("enum_sys.out.3")
self.assertEqual(
enum_sys(groupfile, concs, a_cons, num_wanted, HNF, params, True),
out)
def _enum_out(args):
"""Produce the enumerations of a subset of the total number of possible
arrangements for the desired HNFs. It assumes that all the information
used in the polya part above is still available.
Args:
args (dict): The command line inputs.
"""
import phenum.io_utils as io
import phenum.phonons as pb
from phenum.msg import verbosity
from random import seed
from phenum.grouptheory import get_full_HNF, SmithNormalForm
from os.path import isfile
from glob import glob
from copy import deepcopy
if args["seed"] is not None:
seed(a=args["seed"])
keep_supers = False
if args["super"]:
keep_supers = True
params = io.read_lattice(args["lattice"])
if not isfile(args["input"]):
if not len(glob("polya.out.*")) >= 1:
temp_args = deepcopy(args)
temp_args["outfile"] = "polya.out"
_polya_out(temp_args)
temp_args = deepcopy(args)
temp_args["input"] = "polya.out"
temp_args["outfile"] = args["input"]
if args["distribution"] is None:
temp_args["distribution"] = ["all", "all"]
else:
temp_args["distribution"] = args["distribution"]
_enum_in(temp_args)
systems = io.read_enum(args["input"])
io.write_enum(params, outfile=args["outfile"])
count_t = 1
count_s = 0
from operator import itemgetter
sfmt = (
"{0: >10d}{1: >10d}{2: >8d}{3: >9d}{4: >9d}{5: >12d}{6: >4d}{7: >6d}"
"{8: >10} {9: >18} {10: >44} {11} {12: >21}\n")
def fmtn(l, n):
l = [int(i) for i in l]
return (''.join([
"{{{0:d}: >{1:d}d}}".format(i, n) for i in range(len(l))
])).format(*l)
with open(args["outfile"], 'a') as f:
enumlist = []
for hnf, conc, num_wanted in systems:
if verbosity is not None and verbosity >= 1: #pragma: no cover
from tqdm import tqdm
pbar = tqdm(total=len(systems))
(SNF, L, R) = SmithNormalForm(get_full_HNF(hnf))
SNF = [SNF[0][0], SNF[1][1], SNF[2][2]]
LT = [item for row in L for item in row]
a_concs = pb.get_arrow_concs(params)
configs = pb.enum_sys(None, list(conc), a_concs, num_wanted, hnf,
params, keep_supers, args["acceptrate"])
for config in configs:
labeling, arrowing = io.create_labeling(config)
enumlist.append(((hnf[0] * hnf[2] * hnf[5]), hnf, SNF, LT,
labeling, arrowing))
sortenum = sorted(enumlist, key=itemgetter(0, 4))
if len(sortenum) > 0:
last_sz = sortenum[0][0]
if verbosity is not None and verbosity >= 1: #pragma: no cover
pbar.update(1)
for (size, hnf, SNF, LT, labeling, arrowing) in sortenum:
if size != last_sz:
count_s = 1
last_sz = size
else:
count_s += 1
o = sfmt.format(count_t, 1, 1, 1, 1,
count_s, size, 1, fmtn(SNF, 3), fmtn(hnf, 3),
fmtn(LT, 5), labeling, arrowing)
f.write(o)
count_t += 1