def correlation(self):
m = self.m
if not tl.exists("jin.npy"):
print("loading jin.txt")
j = np.loadtxt('jin.txt', skiprows=2)[:, 1]
np.save('jin.npy', j)
j = np.load('jin.npy')
print("loaded")
n = len(j)
if not tl.exists("jj0.npy"):
jj0 = acf(j)[:n / 2 + 1]
np.save('jj0.npy', jj0)
jj0 = np.load('jj0.npy')[:m.aveRate]
xlo, xhi, ylo, yhi, zlo, zhi, lx, ly, lz = m.box
v = lx * ly * lz
factor = m.corRate * m.timestep / \
(v * m.kb * m.T * m.T) * m.zfactor * m.tcfactor
x = range(len(jj0))
plot([x, 'Correlation Time (ps)'],
[jj0, 'Heat Flut Correlation Function'], 'acf.png')
plot([x, 'Correlation Time (ps)'],
[jj0.cumsum() * factor, 'Thermal Conductivity (W/mK)'],
'kappa.png')
def writePOTCAR(options, elements):
dir = 'pot' # LDA
# paw：PAW-LDA
# paw_gga：PAW-GGA-PW91
# paw_pbe：PAW-GGA-PBE
# pot：USPP-LDA
# pot_GGA：USPP-GGA
if not options.paw:
if options.gga:
dir = 'pot_GGA'
else:
dir = 'pot'
else:
if not options.gga:
dir = 'paw'
else:
if options.pbe:
dir = 'paw_pbe'
else:
dir = 'paw_gga'
tl.passthru('cat "" >POTCAR')
for ele in elements:
file = config.vasppot + "/%s/%s/POTCAR" % (dir, ele)
z = False
if not tl.exists(file):
file += '.Z'
z = True
assert tl.exists(file)
if z:
tl.passthru('zcat %s >> POTCAR' % file)
else:
tl.passthru('cat %s >> POTCAR' % file)
def __init__(self):
"""
while not os.path.exists('app.json'):
time.sleep(1)
print pwd()+'/app.json'
"""
if tl.exists('app.json'):
opt = tl.loadjson('app.json')
elif tl.exists('../app.json'):
opt = tl.loadjson('../app.json')
elif tl.exists('../../app.json'):
opt = tl.loadjson('../../app.json')
elif tl.exists('../../../app.json'):
opt = tl.loadjson('../../../app.json')
else:
tl.exit('app.json lost!')
species = opt['species']
s = im('aces.materials.%s' % species)
m = s.structure(opt)
self.m = m
m.home = tl.pwd()
assert m.home != ''
Runner = im('aces.runners.%s' % m.runner)
self.runner = Runner.runner(m)
def writePOTCAR(options, elements):
dir = 'pot' # LDA
# paw：PAW-LDA
# paw_gga：PAW-GGA-PW91
# paw_pbe：PAW-GGA-PBE
# pot：USPP-LDA
# pot_GGA：USPP-GGA
if not options.paw:
if options.gga:
dir = 'pot_GGA'
else:
dir = 'pot'
else:
if not options.gga:
dir = 'paw'
else:
if options.pbe:
dir = 'paw_pbe'
else:
dir = 'paw_gga'
tl.passthru('cat "" >POTCAR')
for ele in elements:
file = config.vasppot + "/%s/%s/POTCAR" % (dir, ele)
z = False
if not tl.exists(file):
file += '.Z'
z = True
assert tl.exists(file)
if z:
tl.passthru('zcat %s >> POTCAR' % file)
else:
tl.passthru('cat %s >> POTCAR' % file)
def check(self):
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
tl.debug('entering loop waiting for vasp...')
while not jobdone.all():
time.sleep(3)
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
# debug(paths[jobdone])
tl.debug('done')
def check(self):
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
tl.debug('entering loop waiting for vasp...')
while not jobdone.all():
time.sleep(3)
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
# debug(paths[jobdone])
tl.debug('done')
def getsatoms(self):
filename = 'disp_fc3.yaml'
if (tl.exists(filename)):
return disp2atoms(filename)
filename = 'disp.yaml'
if (tl.exists(filename)):
return disp2atoms(filename)
filename = '3RD.SPOSCAR'
if (tl.exists(filename)):
from ase import io
return io.read(filename, format='vasp')
filename = 'SPOSCAR'
if (tl.exists(filename)):
from ase import io
return io.read(filename, format='vasp')
def reduce(self, nd, *pn):
from aces.qpointsyaml import phononyaml
pya = phononyaml("qpoints/qpoints.yaml")
nq = pya.nqpoint
nbr = pya.nbranch
import h5py
nma = h5py.File('lifenma.h5')
q = np.array(nma['/q/0/0'])
n = len(q)
v = np.zeros([nq * nbr, n])
def onedir(dir, num):
for idir in num:
print(idir)
nma = h5py.File(dir + '/%d/lifenma.h5' % idir)
for i in range(nq):
for j in range(nbr):
node = '/q/%d/%d' % (i, j)
v[i * nbr + j, :] += np.array(nma[node])
return len(num)
N = 0
for i in range(nd):
dir, num = pn[i * 2:i * 2 + 2]
N += onedir(dir, num)
# N+=onedir('../q3.1',30)
# N+=onedir('../q3.2',90)
v /= N
if tl.exists('phis.h5'):
tl.passthru('rm phis.h5')
phis = h5py.File('phis.h5')
for i in range(nq):
for j in range(nbr):
node = '/%d/%d' % (i, j)
phis[node] = v[i * nbr + j, :]
def check(self, filename='FORCE_CONSTANTS'):
ref = io.read('SPOSCAR')
files = shell_exec("ls dirs").split('\n')
fc2 = readfc2(filename)
np.set_printoptions(precision=2, suppress=True)
vasprunxml = "dir_SPOSCAR/vasprun.xml"
if exists(vasprunxml):
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces0 = parseVasprun(vasprun, 'forces')
print(forces0.max())
else:
forces0 = 0.0
for file in files:
print(file)
POSCAR = 'dirs/%s/POSCAR' % file
vasprunxml = "dirs/%s/vasprun.xml" % file
atoms = io.read(POSCAR)
u = atoms.positions - ref.positions
f = -np.einsum('ijkl,jl', fc2, u)
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces = parseVasprun(vasprun, 'forces') - forces0
print(np.abs(f).max(), "\n")
print(np.abs(forces - f).max())
print(np.allclose(f, forces, atol=1e-2))
def reduce(self, nd, *pn):
from aces.qpointsyaml import phononyaml
pya = phononyaml("qpoints/qpoints.yaml")
nq = pya.nqpoint
nbr = pya.nbranch
import h5py
nma = h5py.File('lifenma.h5')
q = np.array(nma['/q/0/0'])
n = len(q)
v = np.zeros([nq * nbr, n])
def onedir(dir, num):
for idir in num:
print(idir)
nma = h5py.File(dir + '/%d/lifenma.h5' % idir)
for i in range(nq):
for j in range(nbr):
node = '/q/%d/%d' % (i, j)
v[i * nbr + j, :] += np.array(nma[node])
return len(num)
N = 0
for i in range(nd):
dir, num = pn[i * 2:i * 2 + 2]
N += onedir(dir, num)
# N+=onedir('../q3.1',30)
# N+=onedir('../q3.2',90)
v /= N
if tl.exists('phis.h5'):
tl.passthru('rm phis.h5')
phis = h5py.File('phis.h5')
for i in range(nq):
for j in range(nbr):
node = '/%d/%d' % (i, j)
phis[node] = v[i * nbr + j, :]
def checkParent(dir, n=0):
if n == 5: raise Exception('error when find sub.py')
if not exists(dir + '/sub.py'):
dir = realpath(dir + '/..')
return checkParent(dir, n + 1)
else:
return dir
def check(self, filename='FORCE_CONSTANTS'):
ref = io.read('SPOSCAR')
files = shell_exec("ls dirs").split('\n')
fc2 = readfc2(filename)
np.set_printoptions(precision=2, suppress=True)
vasprunxml = "dir_SPOSCAR/vasprun.xml"
if exists(vasprunxml):
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces0 = parseVasprun(vasprun, 'forces')
print(forces0.max())
else:
forces0 = 0.0
for file in files:
print(file)
POSCAR = 'dirs/%s/POSCAR' % file
vasprunxml = "dirs/%s/vasprun.xml" % file
atoms = io.read(POSCAR)
u = atoms.positions - ref.positions
f = -np.einsum('ijkl,jl', fc2, u)
vasprun = etree.iterparse(vasprunxml, tag='varray')
forces = parseVasprun(vasprun, 'forces') - forces0
print(np.abs(f).max(), "\n")
print(np.abs(forces - f).max())
print(np.allclose(f, forces, atol=1e-2))
def checkParent(dir, n=0):
if n == 5:
raise Exception('error when find sub.py')
if not exists(dir + '/sub.py'):
dir = realpath(dir + '/..')
return checkParent(dir, n + 1)
else:
return dir
def runbol(self):
self.getwin()
p = config.espresso + "bin/postw90.x"
if not tl.exists(p):
print("p not exists")
return
postw90 = self.getx("postw90", pool=False)
tl.passthru(postw90 + " diam")
def runbol(self):
self.getwin()
p = config.espresso + "bin/postw90.x"
if not tl.exists(p):
print("p not exists")
return
postw90 = self.getx("postw90", pool=False)
tl.passthru(postw90 + " diam")
def rerunepw(self):
m = self.m
subcores = m.cores
if not tl.exists('epw.in'):
self.getepwin()
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw.in > epw.out"
tl.passthru(cmd3)
def rerunepw(self):
m = self.m
subcores = m.cores
if not tl.exists('epw.in'):
self.getepwin()
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw.in > epw.out"
tl.passthru(cmd3)
def lifenmaq(self, filename="qpoints/qpoints.yaml",
k=[0, 0, 0], correlation_supercell=[10, 10, 1], test=False):
self.test = test
self.pfactor = self.getpfactor(correlation_supercell)
pya = phononyaml(filename)
self.pya = pya
self.testk = k
if not tl.exists('NMA'):
tl.mkdir('NMA')
self.specialk(pya, map(float, k))
def parse(self, f, filename):
npy = filename + '.npy'
if self.cache and exists(npy): return np.load(npy)
print "scanning the file %s" % filename
_line = [0]
while f.readline():
_line.append(f.tell())
del _line[-1]
if self.cache:
np.save(npy, _line)
return _line
def info(self):
if not exists('velocity.info'):
self.prepare()
s=read('velocity.info').split()
self.natom=int(s[0])
self.totalStep=int(s[1])
self.timestep=float(s[2])
self.times=np.arange(self.totalStep)*self.timestep
maxFreq=1/2.0/self.timestep
self.freq=np.linspace(0,1,self.totalStep/2)*maxFreq
return self.natom,self.totalStep,self.timestep,self.freq,self.times
def getV(self):
if not exists('groupv'):
mkdir('groupv')
cd('groupv')
cp('../FORCE_CONSTANTS', '.')
cp('../POSCAR', '.')
cp('../disp.yaml', '.')
self.generate_vconf()
passthru(config.phonopy + "--tolerance=1e-4 v.conf")
self.drawV()
cd('..')
def get_eigs(file="mesh.npz"):
if not tl.exists(file):
name = file.replace('npz', 'yaml')
print("generate " + file)
data = meshyaml(name)
np.savez(file, **data)
data = np.load(file)
freqs = data['frequency']
eigs = data['eigs']
qpoints = data['qpoints']
return qpoints, freqs, eigs
def getV(self):
if not exists('groupv'):
mkdir('groupv')
cd('groupv')
cp('../FORCE_CONSTANTS', '.')
cp('../POSCAR', '.')
cp('../disp.yaml', '.')
self.generate_vconf()
passthru(config.phonopy + "--tolerance=1e-4 v.conf")
self.drawV()
cd('..')
def parse(self, f, filename):
npy = filename + '.npy'
if self.cache and exists(npy):
return np.load(npy)
print("scanning the file %s" % filename)
_line = [0]
while f.readline():
_line.append(f.tell())
del _line[-1]
if self.cache:
np.save(npy, _line)
return _line
def minimize(self):
if (self.m.copyN == -1):
copymini = False
else:
copymini = True
if copymini:
while not tl.exists('../%d/minimize/done' % self.m.copyN):
tl.sleep(30)
print('copymini')
tl.cp('../%d/minimize' % self.m.copyN, '.')
else:
self.creatmini()
def force_constant(self, files):
cmd = config.phonopy + "-f "
if exists("dir_SPOSCAR/vasprun.xml"):
cmd = config.phonopy + "--fz dir_SPOSCAR/vasprun.xml "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
# generate FORCE_SETS
passthru(cmd)
m = self.m
# Create FORCE_CONSTANTS
passthru(config.phonopy + "--tolerance=1e-4 --writefc --dim='%s'" %
(m.dim))
def force_constant(self, files):
cmd = config.phonopy + "-f "
if exists("dir_SPOSCAR/vasprun.xml"):
cmd = config.phonopy + "--fz dir_SPOSCAR/vasprun.xml "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
# generate FORCE_SETS
passthru(cmd)
m = self.m
# Create FORCE_CONSTANTS
passthru(config.phonopy + "--tolerance=1e-4 --writefc --dim='%s'" %
(m.dim))
def lifenmaq(self,
filename="qpoints/qpoints.yaml",
k=[0, 0, 0],
correlation_supercell=[10, 10, 1],
test=False):
self.test = test
self.pfactor = self.getpfactor(correlation_supercell)
pya = phononyaml(filename)
self.pya = pya
self.testk = k
if not tl.exists('NMA'):
tl.mkdir('NMA')
self.specialk(pya, map(float, k))
def allnma(self, filename="qpoints/qpoints.yaml"):
pya = phononyaml(filename)
f = open('allnma.txt', 'w')
f.write('kx\tky\tkz\tfreq\tw0\tscatter\ttao\n')
self.all = True
c = h5py.File('allnma.h5')
assert tl.exists('phis.h5')
self.phis = h5py.File('phis.h5')
for iqp in range(pya.nqpoint):
for ibr in range(pya.nbranch):
node = '/%s/%s' % (iqp, ibr)
print(node)
if node not in c:
k = pya.qposition(iqp)
freq = pya.frequency(iqp, ibr)
vec = pya.atoms(iqp, ibr)
v, q = self.calculateLife((k, freq, vec), iqp, ibr)
c[node] = v
f.write('%s\n' % c[node][()])
def allnma(self, filename="qpoints/qpoints.yaml"):
pya = phononyaml(filename)
f = open('allnma.txt', 'w')
f.write('kx\tky\tkz\tfreq\tw0\tscatter\ttao\n')
self.all = True
c = h5py.File('allnma.h5')
assert tl.exists('phis.h5')
self.phis = h5py.File('phis.h5')
for iqp in range(pya.nqpoint):
for ibr in range(pya.nbranch):
node = '/%s/%s' % (iqp, ibr)
print(node)
if node not in c:
k = pya.qposition(iqp)
freq = pya.frequency(iqp, ibr)
vec = pya.atoms(iqp, ibr)
v, q = self.calculateLife((k, freq, vec), iqp, ibr)
c[node] = v
f.write('%s\n' % c[node][()])
def lmp_structure(self):
import os
file = os.path.join(os.path.dirname(__file__), 'data',
self.poscar + ".POSCAR")
# because file is unicode in default and ase check if file is not str
# then look it as a file
file = str(file)
assert tl.exists(file)
print(file)
atoms = io.read(file)
if not self.type == "zigzag":
newatoms = atoms.copy()
cell = [atoms.cell[1, 1], atoms.cell[0, 0], atoms.cell[2, 2]]
positions = atoms.positions[:, [1, 0, 2]]
newatoms.set_cell(cell)
newatoms.set_positions(positions)
atoms = newatoms
atoms = atoms.repeat([self.latx, self.laty, self.latz])
return atoms
def sed_band(self, correlation_supercell=[10, 10, 1]):
self.pfactor = self.getpfactor(correlation_supercell)
data = tl.parseyaml('band.yaml')
natom_unitcell = int(data['natom'])
if not tl.exists('SEDBAND'):
tl.mkdir('SEDBAND')
sed = []
db = h5py.File('sed.h5')
def u(phonon):
qp = phonon['q-position']
qps = str(qp)
print(qps)
if qps not in db:
db[qps] = self.calculateSED(map(float, qp), natom_unitcell)
s = db[qps][:]
sed.append(s)
map(u, data['phonon'])
totalStep = self.totalStep
x = np.linspace(0, 1, totalStep / 2 + 1) * 1 / 2.0 / self.timestep
np.save('wtick.npy', x)
np.save('sed.npy', sed)
def sed_band(self, correlation_supercell=[10, 10, 1]):
self.pfactor = self.getpfactor(correlation_supercell)
data = tl.parseyaml('band.yaml')
natom_unitcell = int(data['natom'])
if not tl.exists('SEDBAND'):
tl.mkdir('SEDBAND')
sed = []
db = h5py.File('sed.h5')
def u(phonon):
qp = phonon['q-position']
qps = str(qp)
print(qps)
if qps not in db:
db[qps] = self.calculateSED(map(float, qp), natom_unitcell)
s = db[qps][:]
sed.append(s)
map(u, data['phonon'])
totalStep = self.totalStep
x = np.linspace(0, 1, totalStep / 2 + 1) * 1 / 2.0 / self.timestep
np.save('wtick.npy', x)
np.save('sed.npy', sed)
def pix(self, cmd):
if tl.exists('dy.h5'):
v = "-lv dy.h5"
else:
v = "dynaphopy.lammpstrj"
tl.passthru("dynaphopy in.dy %s -ts %f %s" % (v, self.m.timestep, cmd))
def __init__(self,timestep=0.0005):
if exists('velocity.h5md'):
self.db=h5py.File('velocity.h5md')
n = 5
sk = np.zeros_like(s[:, 1])
for j, u in enumerate(s[n:-n]):
sk[j + n] = s[j:j + n, 1].mean()
v = []
n = 30
for j, u in enumerate(sk[n:-n]):
var = abs(sk[j + n] - sk[j + n - 1])
if var > 1.0 and var > sk[j:j + n].std():
if len(v) > 0 and j - v[-1] < n:
continue
v.append(j + n)
return np.array(v)
if not tl.exists('strain/seed1/cache.npz'):
c = []
d = []
i = 0
for seed in range(200, 400):
dir = "strain/seed1/" + str(i)
s = np.loadtxt(dir + "/cal_stress.txt", skiprows=1)
v = getBreakStrains(s)
i += 1
print(dir, s[v, 0])
c.append(s[v, 0])
d.append([s, v])
i = 0
for seed in range(400, 600):
dir = "strain/seed2/" + str(i)
s = np.loadtxt(dir + "/cal_stress.txt", skiprows=1)
def calculateLife(self, eigen, iqp, ibr):
q = self.modeSed(eigen, iqp, ibr)
if tl.exists('velocity.h5md'):
tl.passthru('rm velocity.h5md')
k, freq, vec = eigen
return self.modefit(iqp, ibr, k, freq, q)
def runph(self):
if not tl.exists('ph.in'):
self.getphin()
ph = self.getx("ph")
tl.passthru(ph + " < ph.in > ph.out ")
def runph(self):
if not tl.exists('ph.in'):
self.getphin()
ph = self.getx("ph")
tl.passthru(ph + " < ph.in > ph.out ")
def getfcs(self):
tl.passthru(config.alm + "< fit.in > fit.out")
assert tl.exists("alm.fcs")
assert tl.exists("alm.xml")
def getfcs(self):
tl.passthru(config.alm + "< fit.in > fit.out")
assert tl.exists("alm.fcs")
assert tl.exists("alm.xml")
def cal_lc(self, r, dr, m):
from aces.lammpsdata import lammpsdata
atoms = lammpsdata().set_src('correlation_structure')
atoms.set_pbc([m.xp, m.yp, m.zp])
nw = self.totalStep / 2 + 1
nr = int(r / dr) + 1
n = len(atoms)
pos = atoms.positions
cell = atoms.cell
symbols = atoms.get_chemical_symbols()
masses = self.getMassFromLabel(symbols)
if not tl.exists('g.npz'):
g = np.zeros([nw, nr], dtype=np.complex)
ng = np.zeros(nr, dtype=np.int)
c = self.get_nei(r, dr, pos, cell)
for i, j, q in c:
if j == 0:
print("center atom:%d/%d" % (i, n))
aij = np.einsum(
'ij,ij->i',
self.fourier_atom(i).conjugate(),
self.fourier_atom(j))
aii = np.einsum(
'ij,ij->i',
self.fourier_atom(i).conjugate(),
self.fourier_atom(i))
ajj = np.einsum(
'ij,ij->i',
self.fourier_atom(j).conjugate(),
self.fourier_atom(j))
x = aij / np.sqrt(aii * ajj) * np.sqrt(masses[i] * masses[j])
for ir in q:
g[:, ir] += x
ng[ir] += 1
np.savez('g.npz', g=g, ng=ng)
npz = np.load('g.npz')
g = npz['g']
ng = npz['ng']
rs = (np.arange(nr)) * dr
rs = rs[:-1]
def aa(x):
if x > 0:
return 1.0 / x
else:
return 0.0
ivr = [aa(x) for x in ng] # 1.0/4.0/np.pi/rs**2
g = np.einsum('ij,j->ij', g, ivr)[:, :-1]
g = (g.conjugate() * g).real
imshow(g, 'g.png', extent=[0, 1, 0, 1])
data = []
for i in range(0, self.totalStep / 2 + 1, self.totalStep / 20):
data.append([rs, g[i, :], str(i)])
series(xlabel='length (A)',
ylabel='Cross Phonon Energy Spectrum',
datas=data, linewidth=2, filename='cpes.png')
cg = g.cumsum(axis=1)
imshow(cg, 'cg.png', extent=[0, 1, 0, 1])
cg = np.einsum('ij,i->ij', cg, 1.0 / cg[:, -1])
data = []
for i in range(0, self.totalStep / 2 + 1, self.totalStep / 10):
data.append([rs, cg[i, :], str(i)])
series(xlabel='length (A)',
ylabel='Cross Phonon Energy Spectrum',
datas=data, linewidth=2, filename='cges.png')
lc = ((cg < 0.80).sum(axis=1)) * dr
x = np.linspace(0, 1, self.totalStep / 2 + 1) * 1 / 2.0 / self.timestep
plot([x, 'Frequency (THz)'], [lc, 'Coherence length(A)'], 'coherence.png')
return lc
def v2h5(self):
if not tl.exists('dy.h5'):
self.pix('-sv dy.h5')
def runnscf(self):
if not tl.exists('nscf.in'):
self.getnscfin()
pw = self.getx("pw")
tl.passthru(pw + " <nscf.in > nscf.out")
def calculateLife(self, eigen, iqp, ibr):
q = self.modeSed(eigen, iqp, ibr)
if tl.exists('velocity.h5md'):
tl.passthru('rm velocity.h5md')
k, freq, vec = eigen
return self.modefit(iqp, ibr, k, freq, q)
def runnscf(self):
if not tl.exists('nscf.in'):
self.getnscfin()
pw = self.getx("pw")
tl.passthru(pw + " <nscf.in > nscf.out")
def pix(self, cmd):
if tl.exists('dy.h5'):
v = "-lv dy.h5"
else:
v = "dynaphopy.lammpstrj"
tl.passthru("dynaphopy in.dy %s -ts %f %s" % (v, self.m.timestep, cmd))
def v2h5(self):
if not tl.exists('dy.h5'):
self.pix('-sv dy.h5')
def allnmaq(self, filename="qpoints/qpoints.yaml", k=[0, 0, 0]):
self.all = True
assert tl.exists('phis.h5')
self.phis = h5py.File('phis.h5')
self.lifenmaq(filename, k)
def cal_lc(self, r, dr, m):
from aces.lammpsdata import lammpsdata
atoms = lammpsdata().set_src('correlation_structure')
atoms.set_pbc([m.xp, m.yp, m.zp])
nw = self.totalStep / 2 + 1
nr = int(r / dr) + 1
n = len(atoms)
pos = atoms.positions
cell = atoms.cell
symbols = atoms.get_chemical_symbols()
masses = self.getMassFromLabel(symbols)
if not tl.exists('g.npz'):
g = np.zeros([nw, nr], dtype=np.complex)
ng = np.zeros(nr, dtype=np.int)
c = self.get_nei(r, dr, pos, cell)
for i, j, q in c:
if j == 0:
print("center atom:%d/%d" % (i, n))
aij = np.einsum('ij,ij->i',
self.fourier_atom(i).conjugate(),
self.fourier_atom(j))
aii = np.einsum('ij,ij->i',
self.fourier_atom(i).conjugate(),
self.fourier_atom(i))
ajj = np.einsum('ij,ij->i',
self.fourier_atom(j).conjugate(),
self.fourier_atom(j))
x = aij / np.sqrt(aii * ajj) * np.sqrt(masses[i] * masses[j])
for ir in q:
g[:, ir] += x
ng[ir] += 1
np.savez('g.npz', g=g, ng=ng)
npz = np.load('g.npz')
g = npz['g']
ng = npz['ng']
rs = (np.arange(nr)) * dr
rs = rs[:-1]
def aa(x):
if x > 0:
return 1.0 / x
else:
return 0.0
ivr = [aa(x) for x in ng] # 1.0/4.0/np.pi/rs**2
g = np.einsum('ij,j->ij', g, ivr)[:, :-1]
g = (g.conjugate() * g).real
imshow(g, 'g.png', extent=[0, 1, 0, 1])
data = []
for i in range(0, self.totalStep / 2 + 1, self.totalStep / 20):
data.append([rs, g[i, :], str(i)])
series(xlabel='length (A)',
ylabel='Cross Phonon Energy Spectrum',
datas=data,
linewidth=2,
filename='cpes.png')
cg = g.cumsum(axis=1)
imshow(cg, 'cg.png', extent=[0, 1, 0, 1])
cg = np.einsum('ij,i->ij', cg, 1.0 / cg[:, -1])
data = []
for i in range(0, self.totalStep / 2 + 1, self.totalStep / 10):
data.append([rs, cg[i, :], str(i)])
series(xlabel='length (A)',
ylabel='Cross Phonon Energy Spectrum',
datas=data,
linewidth=2,
filename='cges.png')
lc = ((cg < 0.80).sum(axis=1)) * dr
x = np.linspace(0, 1, self.totalStep / 2 + 1) * 1 / 2.0 / self.timestep
plot([x, 'Frequency (THz)'], [lc, 'Coherence length(A)'],
'coherence.png')
return lc
def allnmaq(self, filename="qpoints/qpoints.yaml", k=[0, 0, 0]):
self.all = True
assert tl.exists('phis.h5')
self.phis = h5py.File('phis.h5')
self.lifenmaq(filename, k)
