def test_1(self):
from phenum.phonons import arrow_concs
cList = [1, 2, 1]
aconcs = [0, 0.4245868629437351, 0]
self.assertEqual(arrow_concs(cList,aconcs),[[-1, 1], [-1, 3], [-1, 2], [-1, 2]])
def test_2(self):
from phenum.phonons import arrow_concs
cList = [3]
aconcs = [0.8205195542173467]
out = [[-1, 1], [1, 1], [1, 1]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_5(self):
from phenum.phonons import arrow_concs
cList = [3]
aconcs = [0.2871674398220775]
out = [[-1, 1], [-1, 1], [-1, 1]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_6(self):
from phenum.phonons import arrow_concs
cList = [3, 1]
aconcs = [0.32514696876724436, 0]
out = [[-1, 2], [-1, 1], [-1, 1], [-1, 1]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_1(self):
from phenum.phonons import arrow_concs
cList = [1, 2, 1]
aconcs = [0, 0.4245868629437351, 0]
self.assertEqual(arrow_concs(cList, aconcs),
[[-1, 1], [-1, 3], [-1, 2], [-1, 2]])
def test_12(self):
from phenum.phonons import arrow_concs
cList = [3, 0, 2]
aconcs = [0, 0, 0.5]
out = [[-1, 3], [-1, 1], [-1, 1], [-1, 1], [1, 3]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_2(self):
from phenum.phonons import arrow_concs
cList = [3]
aconcs = [0.8205195542173467]
out = [[-1, 1], [1, 1], [1, 1]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_11(self):
from phenum.phonons import arrow_concs
cList = [2, 0, 1]
aconcs = [0,0,0]
out = [[-1, 3], [-1, 1], [-1,1]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_12(self):
from phenum.phonons import arrow_concs
cList = [3, 0, 2]
aconcs = [0,0,0.5]
out = [[-1, 3], [-1, 1], [-1, 1], [-1, 1], [1, 3]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_6(self):
from phenum.phonons import arrow_concs
cList = [3, 1]
aconcs = [0.32514696876724436, 0]
out = [[-1, 2], [-1, 1], [-1, 1], [-1, 1]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_5(self):
from phenum.phonons import arrow_concs
cList = [3]
aconcs = [0.2871674398220775]
out = [[-1, 1], [-1, 1], [-1, 1]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_11(self):
from phenum.phonons import arrow_concs
cList = [2, 0, 1]
aconcs = [0, 0, 0]
out = [[-1, 3], [-1, 1], [-1, 1]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_4(self):
from phenum.phonons import arrow_concs
cList = [2, 4, 1, 5, 2, 1, 1]
aconcs = [0.9068065455664464, 0.2858477549741846, 0, 0, 0.6957735268097871, 0, 0]
out = [[-1, 1], [-1, 3], [-1, 5], [-1, 6], [-1, 7], [-1, 2], [-1, 2], [-1, 2], [-1, 4],
[-1, 4], [-1, 4], [-1, 4], [-1, 4], [1, 1], [1, 2], [1, 5]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_8(self):
from phenum.phonons import arrow_concs
cList = [2, 8, 3, 1]
aconcs = [0.8244881520042212, 0.33517966472359717, 0.677253228566329, 0]
out = [[-1, 1], [-1, 3], [-1, 4], [-1, 2], [-1, 2], [-1, 2], [-1, 2], [-1, 2], [-1, 2],
[1, 1], [1, 2], [1, 2], [1, 3], [1, 3]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_3(self):
from phenum.phonons import arrow_concs
cList = [10, 3, 1]
aconcs = [0, 0.4989661535030203, 0]
out = [[-1, 3], [-1, 2], [-1, 2], [-1, 1], [-1, 1], [-1, 1], [-1, 1],
[-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 1], [1, 2]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_3(self):
from phenum.phonons import arrow_concs
cList = [10, 3, 1]
aconcs = [0, 0.4989661535030203, 0]
out = [[-1, 3], [-1, 2], [-1, 2], [-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 1], [-1, 1],
[-1, 1], [-1, 1], [-1, 1], [-1, 1], [1, 2]]
self.assertEqual(arrow_concs(cList,aconcs),out)
def test_8(self):
from phenum.phonons import arrow_concs
cList = [2, 8, 3, 1]
aconcs = [
0.8244881520042212, 0.33517966472359717, 0.677253228566329, 0
]
out = [[-1, 1], [-1, 3], [-1, 4], [-1, 2], [-1, 2], [-1, 2], [-1, 2],
[-1, 2], [-1, 2], [1, 1], [1, 2], [1, 2], [1, 3], [1, 3]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def test_4(self):
from phenum.phonons import arrow_concs
cList = [2, 4, 1, 5, 2, 1, 1]
aconcs = [
0.9068065455664464, 0.2858477549741846, 0, 0, 0.6957735268097871,
0, 0
]
out = [[-1, 1], [-1, 3], [-1, 5], [-1, 6], [-1, 7], [-1, 2], [-1, 2],
[-1, 2], [-1, 4], [-1, 4], [-1, 4], [-1, 4], [-1, 4], [1, 1],
[1, 2], [1, 5]]
self.assertEqual(arrow_concs(cList, aconcs), out)
def _polya_out(args):
"""Generates the 'polya.out' files for the cell sizes specified in 'lattice.in'
(or other specified input file).
Args:
args (dict): The command line inputs.
"""
from phenum.HNFs import get_HNFs
from phenum.grouptheory import get_sym_group
from phenum.symmetry import get_concs_for_size
from phenum.io_utils import read_lattice
import phenum.phonons as pb
from phenum.polyaburnside import polya
params = read_lattice(args["lattice"])
for s in range(params["sizes"][0], params["sizes"][1]+1):
# get HNFs
hnfs = get_HNFs(s,params["lat_vecs"],params["basis_vecs"],3)
out = open(args["outfile"]+"."+str(s), 'w+')
# find the concentrations available for the desired cell sizes.
c_list = get_concs_for_size(s, params["nspecies"], params["is_crestricted"],
len(params["basis_vecs"]), params["concs"])
# We need to write the concs in c_list to the output file.
out.write('{0: <28}'.format("# HNF"))
for conc in c_list:
out.write("{0: <50}".format(':'.join(map(str, conc))))
out.write('{0: <50}\n'.format("Total"))
a_concs = pb.get_arrow_concs(params)
conc_totals = [0 for i in range(len(c_list))]
for thnf in hnfs:
hnf = [thnf[0][0],thnf[1][0],thnf[1][1],thnf[2][0],thnf[2][1],thnf[2][2]]
out.write(" {0: <26}".format(' '.join(map(str, hnf))))
sym_g = get_sym_group(params["lat_vecs"],params["basis_vecs"],thnf,3)
agroup = []
len_sym_g = len(sym_g.perm.site_perm)
for i in range(len_sym_g):
agroup.append([sym_g.perm.site_perm[i],sym_g.perm.arrow_perm[i]])
# we need to loop over the concentrations and find the
# number of arrangements possible for each cell size
total = 0
for iconc, conc in enumerate(c_list):
if len(conc) > 0:
decorations = pb.arrow_concs(conc,a_concs)
# we need to know the concentrations of the
# species with and without arrows, we also need to
# know the number of arrows and their species so
# we can undo the previous step later
(n_arrows,arrow_types,concs_w_arrows) = pb.how_many_arrows(decorations)
# now find the number of unique arrangements using Polya.
if arrow_types != 0 or n_arrows !=0:
total_num = polya(concs_w_arrows,agroup,arrowings=arrow_types)
else:
total_num = polya(conc, agroup)
out.write("{0: <50d}".format(total_num))
total += total_num
conc_totals[iconc] += total_num
out.write('{0: <10d}\n'.format(total))
out.write("# " + ''.join(['-' for i in range(len(c_list)*10 + 10 + 30)]) + '\n')
out.write("{0: <28}".format(" 0 0 0 0 0 0"))
for ctotal in conc_totals:
out.write("{0: <50d}".format(ctotal))
out.write("{0: <50d}\n".format(sum(conc_totals)))
out.close()
def _polya_out(args):
"""Generates the 'polya.out' files for the cell sizes specified in 'lattice.in'
(or other specified input file).
Args:
args (dict): The command line inputs.
"""
from phenum.HNFs import get_HNFs
from phenum.grouptheory import get_sym_group
from phenum.symmetry import get_concs_for_size
from phenum.io_utils import read_lattice
import phenum.phonons as pb
from phenum.polyaburnside import polya
params = read_lattice(args["lattice"])
for s in range(params["sizes"][0], params["sizes"][1] + 1):
# get HNFs
hnfs = get_HNFs(s, params["lat_vecs"], params["basis_vecs"], 3)
out = open(args["outfile"] + "." + str(s), 'w+')
# find the concentrations available for the desired cell sizes.
c_list = get_concs_for_size(s, params["nspecies"],
params["is_crestricted"],
len(params["basis_vecs"]), params["concs"])
# We need to write the concs in c_list to the output file.
out.write('{0: <28}'.format("# HNF"))
for conc in c_list:
out.write("{0: <50}".format(':'.join(map(str, conc))))
out.write('{0: <50}\n'.format("Total"))
a_concs = pb.get_arrow_concs(params)
conc_totals = [0 for i in range(len(c_list))]
for thnf in hnfs:
hnf = [
thnf[0][0], thnf[1][0], thnf[1][1], thnf[2][0], thnf[2][1],
thnf[2][2]
]
out.write(" {0: <26}".format(' '.join(map(str, hnf))))
sym_g = get_sym_group(params["lat_vecs"], params["basis_vecs"],
thnf, 3)
agroup = []
len_sym_g = len(sym_g.perm.site_perm)
for i in range(len_sym_g):
agroup.append(
[sym_g.perm.site_perm[i], sym_g.perm.arrow_perm[i]])
# we need to loop over the concentrations and find the
# number of arrangements possible for each cell size
total = 0
for iconc, conc in enumerate(c_list):
if len(conc) > 0:
decorations = pb.arrow_concs(conc, a_concs)
# we need to know the concentrations of the
# species with and without arrows, we also need to
# know the number of arrows and their species so
# we can undo the previous step later
(n_arrows, arrow_types,
concs_w_arrows) = pb.how_many_arrows(decorations)
# now find the number of unique arrangements using Polya.
if arrow_types != 0 or n_arrows != 0:
total_num = polya(concs_w_arrows,
agroup,
arrowings=arrow_types)
else:
total_num = polya(conc, agroup)
out.write("{0: <50d}".format(total_num))
total += total_num
conc_totals[iconc] += total_num
out.write('{0: <10d}\n'.format(total))
out.write("# " +
''.join(['-'
for i in range(len(c_list) * 10 + 10 + 30)]) + '\n')
out.write("{0: <28}".format(" 0 0 0 0 0 0"))
for ctotal in conc_totals:
out.write("{0: <50d}".format(ctotal))
out.write("{0: <50d}\n".format(sum(conc_totals)))
out.close()
