def rotatefc3(t,
direct=[0, 0, 1],
file1='FORCE_CONSTANTS_3RD',
file2='fc3new'):
f = open(file1)
g = open(file2, 'w')
M = rotationMatrix(direct, t * np.pi / 180.0)
nblock = int(f.next().split()[0])
print >> g, nblock
print >> g, ""
for i in range(nblock):
f.next()
print >> g, f.next(),
r1 = np.array(map(float, f.next().split()))
r1t = M.dot(r1)
print >> g, tl.toString(r1t)
r1 = np.array(map(float, f.next().split()))
r1t = M.dot(r1)
print >> g, tl.toString(r1t)
print >> g, f.next(),
fc = np.zeros([3, 3, 3])
for i in range(3):
for j in range(3):
for k in range(3):
fc[i, j, k] = float(f.next().split()[3])
fc = np.einsum('ij,jkl->ikl', M, fc)
fc = np.einsum('ij,kjl->kil', M, fc)
fc = np.einsum('ij,klj->kli', M, fc)
print >> g, matrix3Format(fc)
def phana(self):
from aces.tools import read
m = self.m
bp = m.bandpath
bpp = m.bandpoints
v = ""
for i in range(len(bp) - 1):
v += "%s\n%s\n101\n" % (tl.toString(bpp[bp[i]]),
tl.toString(bpp[bp[i + 1]]))
s = """20
1
2
phana.band.txt
%sq
0
""" % v
s = s.replace(r'^\s+', '')
tl.write(s, 'phana.in')
tl.passthru(config.phana + 'phonon.bin.%d <phana.in' % m.Ctime)
s = read('pdisp.gnuplot')
s = s.replace('pdisp.eps', 'phana.band.eps')
tl.write(s, 'phana.band.gnuplot')
tl.passthru('rm pdisp.gnuplot')
tl.passthru('gnuplot phana.band.gnuplot')
tl.passthru('convert -rotate 90 phana.band.eps phana.band.png')
def rotatefc3(t, direct=[0, 0, 1], file1='FORCE_CONSTANTS_3RD',
file2='fc3new'):
f = open(file1)
g = open(file2, 'w')
M = rotationMatrix(direct, t * np.pi / 180.0)
nblock = int(f.next().split()[0])
print >> g, nblock
print >> g, ""
for i in range(nblock):
f.next()
print >> g, f.next(),
r1 = np.array(map(float, f.next().split()))
r1t = M.dot(r1)
print >> g, tl.toString(r1t)
r1 = np.array(map(float, f.next().split()))
r1t = M.dot(r1)
print >> g, tl.toString(r1t)
print >> g, f.next(),
fc = np.zeros([3, 3, 3])
for i in range(3):
for j in range(3):
for k in range(3):
fc[i, j, k] = float(f.next().split()[3])
fc = np.einsum('ij,jkl->ikl', M, fc)
fc = np.einsum('ij,kjl->kil', M, fc)
fc = np.einsum('ij,klj->kli', M, fc)
print >> g, matrix3Format(fc)
def maps2p(self, i, j, k):
if not hasattr(self, 's2p'):
self.s2p, c, self.celloffset = self.getS2p()
v = self.celloffset
s = tl.toString(v[j] - v[i]) + '\n'
s += tl.toString(v[k] - v[i]) + '\n'
s += '%d %d %d\n' % (self.s2p[i] + 1, self.s2p[j] + 1, self.s2p[k] + 1)
return s
def maps2p(self, i, j, k):
if not hasattr(self, 's2p'):
self.s2p, c, self.celloffset = self.getS2p()
v = self.celloffset
s = tl.toString(v[j] - v[i]) + '\n'
s += tl.toString(v[k] - v[i]) + '\n'
s += '%d %d %d\n' % (self.s2p[i] + 1, self.s2p[j] + 1, self.s2p[k] + 1)
return s
def refinefc3():
f = open('FORCE_CONSTANTS_3RD')
g = open('fc3new', 'w')
nblock = int(f.next().split()[0])
fc3 = []
r1t = []
r2t = []
idx = []
# print >>g,nblock
for i in range(nblock):
f.next()
f.next()
r1 = np.array(map(float, f.next().split()))
r1t.append(r1)
r2 = np.array(map(float, f.next().split()))
r2t.append(r2)
idx.append(map(int, f.next().split()))
fc = np.zeros([3, 3, 3])
for i in range(3):
for j in range(3):
for k in range(3):
fc[i, j, k] = float(f.next().split()[3])
fc3.append(fc)
scale = np.amax(np.abs(fc3))
u = []
for i in range(nblock):
if np.allclose(np.zeros([3, 3, 3]),
fc3[i] / scale, atol=1e-01 * .3):
u.append(False)
else:
u.append(True)
u = np.array(u)
fc3 = np.array(fc3)[u]
r1t = np.array(r1t)[u]
r2t = np.array(r2t)[u]
idx = np.array(idx)[u]
v = np.unique(idx[:, 0])
filters = np.array([idx[:, 0] == c for c in v])
for i, f in enumerate(filters):
a = np.arange(len(idx))[f][0]
fc3[a] -= fc3[f].sum(axis=0)
v = np.unique(idx[:, 1])
filters = np.array([idx[:, 1] == c for c in v])
for i, f in enumerate(filters):
a = np.arange(len(idx))[f][0]
fc3[a] -= fc3[f].sum(axis=0)
nblock = len(fc3)
print >> g, nblock
for i in range(nblock):
print >> g, i + 1
print >> g, tl.toString(np.around(r1t[i], 3))
print >> g, tl.toString(np.around(r2t[i], 3))
print >> g, tl.toString(idx[i])
print >> g, matrix3Format(fc3[i])
def refinefc3():
f = open('FORCE_CONSTANTS_3RD')
g = open('fc3new', 'w')
nblock = int(f.next().split()[0])
fc3 = []
r1t = []
r2t = []
idx = []
# print >>g,nblock
for i in range(nblock):
f.next()
f.next()
r1 = np.array(map(float, f.next().split()))
r1t.append(r1)
r2 = np.array(map(float, f.next().split()))
r2t.append(r2)
idx.append(map(int, f.next().split()))
fc = np.zeros([3, 3, 3])
for i in range(3):
for j in range(3):
for k in range(3):
fc[i, j, k] = float(f.next().split()[3])
fc3.append(fc)
scale = np.amax(np.abs(fc3))
u = []
for i in range(nblock):
if np.allclose(np.zeros([3, 3, 3]), fc3[i] / scale, atol=1e-01 * .3):
u.append(False)
else:
u.append(True)
u = np.array(u)
fc3 = np.array(fc3)[u]
r1t = np.array(r1t)[u]
r2t = np.array(r2t)[u]
idx = np.array(idx)[u]
v = np.unique(idx[:, 0])
filters = np.array([idx[:, 0] == c for c in v])
for i, f in enumerate(filters):
a = np.arange(len(idx))[f][0]
fc3[a] -= fc3[f].sum(axis=0)
v = np.unique(idx[:, 1])
filters = np.array([idx[:, 1] == c for c in v])
for i, f in enumerate(filters):
a = np.arange(len(idx))[f][0]
fc3[a] -= fc3[f].sum(axis=0)
nblock = len(fc3)
print >> g, nblock
for i in range(nblock):
print >> g, i + 1
print >> g, tl.toString(np.around(r1t[i], 3))
print >> g, tl.toString(np.around(r2t[i], 3))
print >> g, tl.toString(idx[i])
print >> g, matrix3Format(fc3[i])
def writedata(self, filename="structure", creatbonds=-1.0):
a = data()
a.title = self.atoms.get_chemical_formula()
unit, rot = self.get_rotated_atoms()
cell = unit.cell
a.headers['xlo xhi'] = [0, cell[0, 0]]
a.headers['ylo yhi'] = [0, cell[1, 1]]
a.headers['zlo zhi'] = [0, cell[2, 2]]
if (cell[1, 0] > cell[0, 0] * 0.5):
cell[1, 0] = cell[0, 0] * 0.5
v = 1.0
if (cell[1, 0] < 0):
v = -1.0
cell[1, 0] = v * int((abs(cell[1, 0])) * 10000) / 10000.0
#print [cell[1,0]/cell[0,0],cell[2,0]/cell[0,0],cell[2,1]/cell[1,1]];
if not np.allclose(
[0, 0, 0], [
cell[1, 0] / cell[0, 0], cell[2, 0] / cell[0, 0],
cell[2, 1] / cell[1, 1]
],
atol=0.01):
a.headers['xy xz yz'] = [cell[1, 0], cell[2, 0], cell[2, 1]]
a.headers['atoms'] = len(self.atoms)
a.headers['atom types'] = len(self.types)
atomsdata = []
for i, atom in enumerate(unit):
x = [i + 1, self.types.index(atom.symbol) + 1] + \
list(atom.position)
if creatbonds > 0.0:
x = [i + 1, 1, self.types.index(atom.symbol) + 1
] + list(atom.position)
atomsdata.append(x)
a.sections['Atoms'] = [toString(x) + '\n' for x in atomsdata]
if creatbonds > 0.0:
dis = unit.get_all_distances(mic=True)
bonds = []
n = 0
for i in range(len(unit)):
for j in range(i):
if dis[i, j] < creatbonds:
n += 1
bonds.append([n, 1, i + 1, j + 1])
a.sections['Bonds'] = [toString(x) + '\n' for x in bonds]
a.headers['bonds'] = len(bonds)
a.headers['bond types'] = 1
a.write(filename)
return rot
def writedata(self, filename="structure", creatbonds=-1.0):
a = data()
a.title = self.atoms.get_chemical_formula()
unit, rot = self.get_rotated_atoms()
cell = unit.cell
a.headers['xlo xhi'] = [0, cell[0, 0]]
a.headers['ylo yhi'] = [0, cell[1, 1]]
a.headers['zlo zhi'] = [0, cell[2, 2]]
if (cell[1, 0] > cell[0, 0] * 0.5):
cell[1, 0] = cell[0, 0] * 0.5
v = 1.0
if (cell[1, 0] < 0):
v = -1.0
cell[1, 0] = v * int((abs(cell[1, 0])) * 10000) / 10000.0
#print [cell[1,0]/cell[0,0],cell[2,0]/cell[0,0],cell[2,1]/cell[1,1]];
if not np.allclose([0, 0, 0], [
cell[1, 0] / cell[0, 0], cell[2, 0] / cell[0, 0],
cell[2, 1] / cell[1, 1]
],
atol=0.01):
a.headers['xy xz yz'] = [cell[1, 0], cell[2, 0], cell[2, 1]]
a.headers['atoms'] = len(self.atoms)
a.headers['atom types'] = len(self.types)
atomsdata = []
for i, atom in enumerate(unit):
x = [i + 1, self.types.index(atom.symbol) + 1] + \
list(atom.position)
if creatbonds > 0.0:
x = [i + 1, 1, self.types.index(atom.symbol) + 1] + list(
atom.position)
atomsdata.append(x)
a.sections['Atoms'] = [toString(x) + '\n' for x in atomsdata]
if creatbonds > 0.0:
dis = unit.get_all_distances(mic=True)
bonds = []
n = 0
for i in range(len(unit)):
for j in range(i):
if dis[i, j] < creatbonds:
n += 1
bonds.append([n, 1, i + 1, j + 1])
a.sections['Bonds'] = [toString(x) + '\n' for x in bonds]
a.headers['bonds'] = len(bonds)
a.headers['bond types'] = 1
a.write(filename)
return rot
def phanados(self):
from aces.tools import read
m = self.m
s = """20
1
1
%s
2
y
1000
y
phana.dos.txt
0
""" % tl.toString(m.kpoints)
s = s.replace(r'^\s+', '')
tl.write(s, 'phana.dos.in')
tl.passthru(config.phana + 'phonon.bin.%d <phana.dos.in' % m.Ctime)
s = read('pdos.gnuplot')
s = s.replace('pdos.eps', 'phana.dos.eps')
tl.write(s, 'phana.dos.gnuplot')
tl.passthru('rm pdos.gnuplot')
tl.passthru('gnuplot phana.dos.gnuplot')
tl.passthru('convert -rotate 90 phana.dos.eps phana.dos.png')
def generate_bandconf(self):
# generate mesh.conf
m = self.m
bp = m.bandpoints
bpath = ' '.join([toString(bp[x]) for x in m.bandpath])
band = """DIM = %s
ATOM_NAME = %s
BAND = %s
BAND_POINTS = 101
FORCE_CONSTANTS = READ
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(m.elements),
bpath, toString(m.premitive.flatten()))
band = band.replace(r'^\s+', '')
write(band, 'band.conf')
def generate_vqconf(self, q):
# generate q.conf
m = self.m
mesh = """DIM = %s
ATOM_NAME = %s
FORCE_CONSTANTS = READ
GROUP_VELOCITY=.TRUE.
QPOINTS=.TRUE.
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(m.elements), toString(m.premitive.flatten()))
mesh = mesh.replace(r'^\s+', '')
write(mesh, 'q.conf')
s = "%s\n" % len(q)
for qq in q:
s += "%s\n" % toString(qq)
write(s, 'QPOINTS')
def generate_bandconf(self):
# generate mesh.conf
m = self.m
bp = m.bandpoints
bpath = ' '.join([toString(bp[x]) for x in m.bandpath])
band = """DIM = %s
ATOM_NAME = %s
BAND = %s
BAND_POINTS = 101
FORCE_CONSTANTS = READ
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(
m.elements), bpath, toString(m.premitive.flatten()))
band = band.replace(r'^\s+', '')
write(band, 'band.conf')
def generate_vqconf(self, q):
# generate q.conf
m = self.m
mesh = """DIM = %s
ATOM_NAME = %s
FORCE_CONSTANTS = READ
GROUP_VELOCITY=.TRUE.
QPOINTS=.TRUE.
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(m.elements), toString(m.premitive.flatten()))
mesh = mesh.replace(r'^\s+', '')
write(mesh, 'q.conf')
s = "%s\n" % len(q)
for qq in q:
s += "%s\n" % toString(qq)
write(s, 'QPOINTS')
def dyinput(self):
m = self.m
f = open('in.dy', 'w')
print >> f, "STRUCTURE FILE POSCAR"
print >> f, tl.pwd() + "/POSCAR"
print >> f, "FORCE SETS"
print >> f, tl.pwd() + "/FORCE_SETS"
# print >>f,"STRUCTURE FILE OUTCAR"
# print >>f,pwd()+"/dynaphopy.lammpstrj"
print >> f, "SUPERCELL MATRIX PHONOPY"
print >> f, " %d 0 0 \n 0 %d 0\n 0 0 %d" % tuple(m.supercell)
print >> f, "BANDS"
bp = m.bandpath
bpp = m.bandpoints
for i in range(len(bp) - 1):
u = "%s %s" % (tl.toString(bpp[bp[i]],
','), tl.toString(bpp[bp[i + 1]], ','))
print >> f, u
f.close()
def dyinput(self):
m = self.m
f = open('in.dy', 'w')
print >> f, "STRUCTURE FILE POSCAR"
print >> f, tl.pwd() + "/POSCAR"
print >> f, "FORCE SETS"
print >> f, tl.pwd() + "/FORCE_SETS"
# print >>f,"STRUCTURE FILE OUTCAR"
# print >>f,pwd()+"/dynaphopy.lammpstrj"
print >> f, "SUPERCELL MATRIX PHONOPY"
print >> f, " %d 0 0 \n 0 %d 0\n 0 0 %d" % tuple(m.supercell)
print >> f, "BANDS"
bp = m.bandpath
bpp = m.bandpoints
for i in range(len(bp) - 1):
u = "%s %s" % (tl.toString(bpp[bp[i]], ','),
tl.toString(bpp[bp[i + 1]], ','))
print >> f, u
f.close()
def getscfin(self):
m = self.m
tmpl = self.getscf_template()
skpoints = "K_POINTS automatic\n%s 1 1 1" % tl.toString(m.ekpoints)
a = """tprnfor = .true.
tstress = .true.
restart_mode = 'from_scratch'
"""
s = tmpl.replace('TYPE', 'scf').replace('CONTROL', a).replace(
'KPOINTS', skpoints)
tl.write(s, 'scf.in')
def getscfin(self):
m = self.m
tmpl = self.getscf_template()
skpoints = "K_POINTS automatic\n%s 1 1 1" % tl.toString(m.ekpoints)
a = """tprnfor = .true.
tstress = .true.
restart_mode = 'from_scratch'
"""
s = tmpl.replace('TYPE',
'scf').replace('CONTROL',
a).replace('KPOINTS', skpoints)
tl.write(s, 'scf.in')
def get_structure(self):
m = self.m
atoms = m.atoms_from_dump('minimize/range')
satoms = atoms.repeat(m.correlation_supercell)
a = lammpsdata(satoms, m.elements)
a.writedata('correlation_structure', self.m.creatbonds)
# psm=premitiveSuperMapper(atoms,satoms)
# s2p,v,=psm.getS2p()
s = "%s %d\n#l1 l2 l3 k tag\n" % (tl.toString(m.correlation_supercell),
len(atoms))
c = m.correlation_supercell
n = 0
for i in range(c[0]):
for j in range(c[1]):
for k in range(c[2]):
for p in range(len(atoms)):
u = [i, j, k, p, n + 1]
s += tl.toString(u) + "\n"
n += 1
tl.write(s, 'phana.map.in')
def getscf_template(self):
m = self.m
pos = ' \n'.join([
'%s ' % (a.symbol) + m.toString(m.atoms.get_scaled_positions()[i])
for i, a in enumerate(m.atoms)
])
mmm = 1.0 # np.abs(m.atoms.cell).max()*2.0
cell = '\n '.join(
[m.toString(m.atoms.cell[i] / mmm) for i in range(3)])
masses = m.getMassFromLabel(m.elements)
pots = self.getPotName()
potentials = [pots[a] for a in m.elements]
atomspecies = '\n'.join(
tl.toString(a) for a in zip(m.elements, masses, potentials))
path = config.qepot
s = """ &control
calculation = 'TYPE'
prefix = 'diam'
wf_collect = .true.
pseudo_dir = '%s'
outdir = './'
CONTROL
etot_conv_thr = 1.0d-5
forc_conv_thr = 1.0d-4
/
&system
ibrav = 0
celldm(1) =%f
nat = %d
ntyp = %d
ecutwfc = 60
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
/
&electrons
diagonalization = 'david'
mixing_beta = 0.7
conv_thr = 1.0d-10
/
ATOMIC_SPECIES
%s
ATOMIC_POSITIONS crystal
%s
KPOINTS
CELL_PARAMETERS alat
%s
""" % (path, mmm / 0.5291772083, len(m.atoms), len(m.elements), atomspecies,
pos, cell)
return s
def getscf_template(self):
m = self.m
pos = ' \n'.join([
'%s ' % (a.symbol) + m.toString(m.atoms.get_scaled_positions()[i])
for i, a in enumerate(m.atoms)
])
mmm = 1.0 # np.abs(m.atoms.cell).max()*2.0
cell = '\n '.join(
[m.toString(m.atoms.cell[i] / mmm) for i in range(3)])
masses = m.getMassFromLabel(m.elements)
pots = self.getPotName()
potentials = [pots[a] for a in m.elements]
atomspecies = '\n'.join(
tl.toString(a) for a in zip(m.elements, masses, potentials))
path = config.qepot
s = """ &control
calculation = 'TYPE'
prefix = 'diam'
wf_collect = .true.
pseudo_dir = '%s'
outdir = './'
CONTROL
etot_conv_thr = 1.0d-5
forc_conv_thr = 1.0d-4
/
&system
ibrav = 0
celldm(1) =%f
nat = %d
ntyp = %d
ecutwfc = 60
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
/
&electrons
diagonalization = 'david'
mixing_beta = 0.7
conv_thr = 1.0d-10
/
ATOMIC_SPECIES
%s
ATOMIC_POSITIONS crystal
%s
KPOINTS
CELL_PARAMETERS alat
%s
""" % (path, mmm / 0.5291772083, len(m.atoms), len(
m.elements), atomspecies, pos, cell)
return s
def generate_vconf(self):
# generate v.conf
m = self.m
mesh = """DIM = %s
ATOM_NAME = %s
MP = %s
FORCE_CONSTANTS = READ
MESH_SYMMETRY = .FALSE.
GROUP_VELOCITY=.TRUE.
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(m.elements), ' '.join(map(
str, m.kpoints)), toString(m.premitive.flatten()))
mesh = mesh.replace(r'^\s+', '')
write(mesh, 'v.conf')
def writevasp(atoms, file='POSCAR'):
f = open(file, 'w')
s = np.array(atoms.get_chemical_symbols())
ss = atoms.get_scaled_positions()
print >> f, 'ACES POSCAR'
print >> f, '1.0'
for x in atoms.cell:
print >> f, tl.toString(x)
# ele=np.unique(s)
ele = []
for a in s:
if a in ele:
continue
ele.append(a)
print >> f, tl.toString(ele)
a = []
# len(s) = natom
p = np.arange(len(s))
for e in ele:
a.append(p[s == e])
# p= 0 1 2 3 4 5
# s= C N N C N C
# a= [[0,3,5],[1,2,4]]
ns = [len(x) for x in a]
# ns =[3,3]
print >> f, tl.toString(ns)
print >> f, 'Direct'
v = []
for x in a:
for u in x:
v.append(u)
print >> f, tl.toString(ss[u])
# v= [0,3,5,1,2,4]
f.close()
x = np.array(v, dtype=np.int).argsort()
np.savetxt('POSCARswap', x)
def generate_vconf(self):
# generate v.conf
m = self.m
mesh = """DIM = %s
ATOM_NAME = %s
MP = %s
FORCE_CONSTANTS = READ
MESH_SYMMETRY = .FALSE.
GROUP_VELOCITY=.TRUE.
PRIMITIVE_AXIS = %s
""" % (m.dim, ' '.join(m.elements), ' '.join(map(str, m.kpoints)),
toString(m.premitive.flatten()))
mesh = mesh.replace(r'^\s+', '')
write(mesh, 'v.conf')
def writevasp(atoms, file='POSCAR'):
f = open(file, 'w')
s = np.array(atoms.get_chemical_symbols())
ss = atoms.get_scaled_positions()
print >>f, 'ACES POSCAR'
print >>f, '1.0'
for x in atoms.cell:
print >>f, tl.toString(x)
# ele=np.unique(s)
ele = []
for a in s:
if a in ele:
continue
ele.append(a)
print >>f, tl.toString(ele)
a = []
# len(s) = natom
p = np.arange(len(s))
for e in ele:
a.append(p[s == e])
# p= 0 1 2 3 4 5
# s= C N N C N C
# a= [[0,3,5],[1,2,4]]
ns = [len(x) for x in a]
# ns =[3,3]
print >>f, tl.toString(ns)
print >>f, 'Direct'
v = []
for x in a:
for u in x:
v.append(u)
print >>f, tl.toString(ss[u])
# v= [0,3,5,1,2,4]
f.close()
x = np.array(v, dtype=np.int).argsort()
np.savetxt('POSCARswap', x)
def getControl(self):
m = self.m
f = open('CONTROL', 'w')
atoms = io.read('../POSCAR') # m.atoms
elements = m.elements
# shengbte needs nelements <=natoms
if len(elements) > len(atoms):
elements = elements[:len(atoms)]
allocations = """&allocations
\tnelements=%d
\tnatoms=%d
\tngrid(:)=%s
&end
""" % (len(elements), len(atoms), toString(m.kpoints))
cell = atoms.cell
types = toString(
[m.elements.index(x) + 1 for x in atoms.get_chemical_symbols()])
pos = ""
for i, atom in enumerate(atoms):
tu = (i + 1, toString(atoms.get_scaled_positions()[i]))
pos += " positions(:,%d)=%s\n" % tu
crystal = """&crystal
lfactor=0.1,
lattvec(:,1)=%s
lattvec(:,2)=%s
lattvec(:,3)=%s
elements=%s
types=%s
%s
scell(:)=%s
&end
""" % (toString(cell[0]), toString(cell[1]), toString(cell[2]),
' '.join(map(lambda x: '"' + x + '"', elements)), types, pos,
m.dim)
parameters = """¶meters
T=%f
scalebroad=1.0
&end
""" % (m.T)
flags = """
&flags
nonanalytic=.TRUE.
nanowires=.FALSE.
&end
"""
f.write(allocations)
f.write(crystal)
f.write(parameters)
f.write(flags)
f.close()
def life(self, k=[0, 0, 0]):
self.pix("-pa -q %s --silent > dylife%s.txt" % tl.toString(k), str(k))
def nma(self, k=[0, 0, 0]):
self.pix("-q %s -sp 'dvnma%s.txt' -r 0 16 2000" %
(tl.toString(k), str(k)))
def nma(self, k=[0, 0, 0]):
self.pix("-q %s -sp 'dvnma%s.txt' -r 0 16 2000" % (tl.toString(k),
str(k)))
def atomdisp(self, direction=[1, 0, 0]):
self.pix(" -sad %s dydisplacement.txt" % (tl.toString(direction)))
def sed(self, k=[0, 0, 0]):
self.pix("-q %s -sw 'dvsed%s.txt' -r 0 50 2000" %
(tl.toString(k), str(k)))
def sed(self, k=[0, 0, 0]):
self.pix("-q %s -sw 'dvsed%s.txt' -r 0 50 2000" % (tl.toString(k),
str(k)))
def __getattr__(self, attr):
if attr == "dim":
return tl.toString(self.supercell)
if attr == "cores":
return int(self.nodes) * int(self.procs)
def __getattr__(self, attr):
if attr == "dim":
return tl.toString(self.supercell)
if attr == "cores":
return int(self.nodes) * int(self.procs)
def life(self, k=[0, 0, 0]):
self.pix("-pa -q %s --silent > dylife%s.txt" % tl.toString(k), str(k))
def atomdisp(self, direction=[1, 0, 0]):
self.pix(" -sad %s dydisplacement.txt" % (tl.toString(direction)))
def getcut(self):
m = self.m
cut = str(m.shengcut / 10.0)
if m.shengcut < 0:
cut = str(m.shengcut)
return " %s %s " % (toString(m.supercell3), cut)
