def getVaspRun_lammps(m):
# generate structure
rot = m.POSCAR2data()
# generate in
content = get_lammps_script(m)
tl.write(content, "in")
# generate dump.force
tl.shell_exec(config.lammps + " < in >log.out")
d, p, d1, p1 = rot
# generate vasprun.xml
f = open('dump.force')
for i in range(9):
f.next()
forces = ""
poses = ""
for line in f:
line = line.split()
force = np.array(map(float, line[1:4]))
pos = np.array(map(float, line[4:8]))
force = RotateVector(force, d1, -p1)
force = RotateVector(force, d, -p)
forces += "<v> %f %f %f </v>\n" % tuple(force)
poses += "<v> %f %f %f </v>\n" % tuple(pos)
vasprun = '<root><calculation><varray name="forces" >\n'
vasprun += forces
vasprun += '</varray>\n<structure><varray name="positions">\n' + poses
vasprun += '</varray></structure></calculation></root>\n'
tl.write(vasprun, 'vasprun.xml')
f.close()
def write(self):
self.atoms.write("CN.xyz")
write_vasp("POSCAR", self.atoms, sort="True", direct=True, vasp5=True)
poscar = open("POSCAR")
unit_cell = UnitCell(poscar)
unit_cell.num_atom_types = len(self.elements)
tools.write(unit_cell.output_lammps(), "structure")
def getTempProfile(self, begin, upP, deta, S, tcfactor, zfactor):
fas = fixAveSpace('tempProfile.txt')
quants = fas.getConvergence(upP + 1, begin)
tools.to_txt(['Temperature(K)', 'Jx'], quants, 'convergenceT.txt')
snapStep = fas.snapStep
dto = dict(log="step\tkappa\n", plots=[])
coord, aveN, aveQuants = fas.iterate(begin, self.kappaConverge,
snapStep, upP, deta, S, tcfactor,
zfactor, dto)
tools.write(dto['log'], 'convergenceK.txt')
series(
'x(Augstrom)',
'temperature(K)',
dto['plots'],
'convergenceT.png',
linewidth=1,
legend=False)
filter = aveN[:] > 1 # at least 1 atom in the bin
aveC = coord[filter]
aveN = aveN[filter]
aveTemp = aveQuants[filter, 0]
avejx = aveQuants[filter, 1]
nbin = len(avejx)
data = np.c_[np.arange(nbin) + 1, aveC, aveN, aveTemp, avejx]
tools.to_txt(['id', 'Coord', 'Count', 'Temp', 'Jx'], data,
'tempAve.txt')
drawTempAve()
return (aveC, aveN, aveTemp, avejx)
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(
bandstructure, filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(
n_electrons=nelect, filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
def prepareet(self):
fermi = self.get_fermi()
nelect = self.get_nelect()
tl.mkcd('et')
tl.cp('../band/SYMMETRY', '.')
tl.cp('../band/EIGENVAL', '.')
tl.cp('../band/POSCAR', '.')
lpfac = 5
if(self.m.soc):
lpfac = 20
s = """VASP
0 1 0 0.0
%f 0.0005 0.40 %f
CALC
%d
BOLTZ
.15
800. 50.
0.
""" % (fermi, nelect, lpfac)
# Format of DOS
# iskip (not presently used) idebug setgap shiftgap
# Fermilevel (eV, please note), energygrid (Ry),\
# energy span around Fermilevel (Ry), No of electrons
# CALC (calculate expansion coeff), NOCALC read from file
# lpfac, number of latt-points per k-point
# run mode (only BOLTZ is supported)
# (efcut) energy range of chemical potential (Ry)
# Tmax, temperature grid
# energyrange of bands given individual \
# DOS output sig_xxx and dos_xxx (xxx is band number)
tl.write(s, "et.intrans")
tl.cd('..')
def drawdos(self):
from aces.ElectronicDOS.electronicdos import ElectronicDOS
doscar = ElectronicDOS()
# orbital_dos = doscar.sum_ms_dos()
# Create a list of each atom type to sum over.
# type_list = []
# n = 0
# for i in range(len(doscar.unit_cell.atom_types)):
# type_list.append([])
# for j in range(doscar.unit_cell.atom_types[i]):
# type_list[i].append(n)
# n += 1
# Sum dos over sets of atoms.
# partial_dos = doscar.sum_site_dos(type_list,orbital_dos)
dos = doscar.write_dos([doscar.tot_dos])
tl.write(dos, 'dos.txt')
dos = np.loadtxt('dos.txt')
f = tl.shell_exec("grep fermi OUTCAR|tail -1")
from aces.scanf import sscanf
f = sscanf(f, "E-fermi : %f XC(G=0):")
with fig("dos.png"):
pl.xlabel("Energy-Ef (eV)")
pl.ylabel("DOS")
pl.plot(dos[:, 0] - f, dos[:, 1], lw=2)
pl.xlim([-4, 4])
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(bandstructure,
filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(n_electrons=nelect,
filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
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 write(self):
self.atoms.write("CN.xyz")
write_vasp("POSCAR",self.atoms,sort="True",direct=True,vasp5=True)
poscar = open("POSCAR")
unit_cell = UnitCell(poscar)
unit_cell.num_atom_types=len(self.elements)
tools.write(unit_cell.output_lammps(),"structure")
def post(self):
import pandas as pd
df = pd.read_csv("strain_stress.txt",
sep=r"[ \t]",
engine="python",
skiprows=2,
header=None)
import numpy as np
df = np.array(df)
strain = df[:, 1] / df[0, 1] - 1
# convert to GPa
# metalE/metalV/(siE/siV)=metalE/siE*siV/metalV=1/u.si.E()*u.si.L()**2
tl.cd('minimize')
self.m.postMini()
tl.cd('..')
pxx = -df[:, 2] * 1e5 * 1e-9 * self.m.zfactor
from aces.graph import plot
plot((strain, 'Strain'), (pxx, 'Stress (GPa)'),
'stress.png',
linewidth=2,
grid=True)
dp = pd.DataFrame()
dp['Strain'] = strain
dp['Stress_GPa'] = pxx
dp.to_csv('cal_stress.txt', sep='\t', index=False, float_format="%f")
from scipy import stats
slope, intercept, r_value, p_value, std_err = stats.linregress(
strain[:50], pxx[:50])
self.YoungsModulus = slope
tl.write(slope, 'YoungsModulus.txt')
def creatmini(self):
print('creatmini')
tl.mkdir('minimize')
tl.cd('minimize')
minimize_input(self.m)
tl.write(time.strftime('%Y-%m-%d %H:%M:%S'), 'done')
tl.cd('..')
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 getVaspRun_vasp(self):
m = self.m
if m.isym:
sym = "ISYM = 1"
else:
sym = "ISYM = 0"
if m.ispin:
spin = "ISPIN =2"
else:
spin = ""
s = """SYSTEM=calculate energy
PREC = High
IBRION = 8
ENCUT = %f
EDIFF = 1.0e-8
ISMEAR = %d; SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
ADDGRID = .TRUE.
LWAVE = .FALSE.
LCHARG = .FALSE.
%s
%s
""" % (self.m.ecut, m.ismear, sym, spin)
s = s.replace(r'^\s+', '')
tl.write(s, 'INCAR')
m = self.m
m.writePOTCAR()
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, m.ekpoints))
s = s.replace(r'^\s+', '')
tl.write(s, 'KPOINTS')
if 'jm' in self.__dict__:
from aces.jobManager import pbs
path = tl.pwd()
if m.queue == "q3.4":
pb = pbs(queue=m.queue,
nodes=12,
procs=4,
disp=m.pbsname,
path=path,
content=config.mpirun + " 48 " + config.vasp +
' >log.out')
else:
pb = pbs(queue=m.queue,
nodes=4,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 48 " + config.vasp +
' >log.out')
self.jm.reg(pb)
else:
tl.shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def writefc2(fc2, filename='FORCE_CONSTANTS_2ND'):
natom = len(fc2)
s = "%d\n" % natom
for i in range(natom):
for j in range(natom):
s += "%d\t%d\n" % (i + 1, j + 1)
s += matrixFormat(fc2[i, j])
tl.write(s, filename)
def thcode(self, files, put):
s = ""
for file in files:
dir = "dirs/dir_" + file
s += "cd %s\n" % (dir)
s += "yhbatch -N 1 aces.pbs\n"
s += "cd ../../\n"
write(s, put + "/runall.sh")
def thcode(self, files, put):
s = ""
for file in files:
dir = "dirs/dir_" + file
s += "cd %s\n" % (dir)
s += "yhbatch -N 1 aces.pbs\n"
s += "cd ../../\n"
write(s, put + "/runall.sh")
def writefc2(fc2, filename='FORCE_CONSTANTS_2ND'):
natom = len(fc2)
s = "%d\n" % natom
for i in range(natom):
for j in range(natom):
s += "%d\t%d\n" % (i + 1, j + 1)
s += matrixFormat(fc2[i, j])
tl.write(s, filename)
def get_bandplot(self):
tl.write("""diam.freq
0 600
band.plot
band.ps
0.0
50.0 0.0""", "plotband.in")
tl.shell_exec(config.espresso +
"bin/plotband.x < plotband.in >plotband.out")
def getnscfin(self):
m = self.m
tmpl = self.getscf_template()
nscfk = self.getNscfKpoints()
aa = '\n'.join([m.toString(a) for a in nscfk])
newskpoints = "K_POINTS crystal\n%d\n%s" % (len(nscfk), aa)
s = tmpl.replace('TYPE', 'nscf').replace('CONTROL', '').replace(
'KPOINTS', newskpoints)
tl.write(s, "nscf.in")
def get_bandplot(self):
tl.write("""diam.freq
0 600
band.plot
band.ps
0.0
50.0 0.0""", "plotband.in")
tl.shell_exec(config.espresso +
"bin/plotband.x < plotband.in >plotband.out")
def writeKPOINTS(kpoints):
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, kpoints))
s = tl.headtrim(s)
tl.write(s, 'KPOINTS')
def prepare(self):
db=self.db['/particles/main/velocity/']
self.natom=db['value'].shape[1]
self.totalStep=db['step'].shape[0]
if self.totalStep%2==1:self.totalStep-=1
print "Atom Number=",self.natom
print "Total step=",self.totalStep
self.timestep=db['time'][1]-db['time'][0]
write('%d %d %f'%(self.natom,self.totalStep,self.timestep),'velocity.info')
def writeKPOINTS(kpoints):
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, kpoints))
s = tl.headtrim(s)
tl.write(s, 'KPOINTS')
def get_fitin(self):
content = tl.read('alm.in').replace('suggest', 'fitting')
fitting = """&fitting
\tNDATA = %d
\tDFILE = disp_all.dat
\tFFILE = force_all.dat
/
""" % self.NDATA
fitting = tl.trimhead(fitting)
tl.write(content + fitting, 'fit.in')
def setUp(self): content="""# Spatial-averaged data for fix temp_profile and group main # Timestep Number-of-bins # Bin Coord Ncount v_temp v_jx 100000 19 1 14.961 0 0 0 2 17.961 0 0 0 3 20.961 10 291.241 -0.00395033 """ write(content,'tmptestlinemanager.txt')
def setUp(self):
content = """# Spatial-averaged data for fix temp_profile and group main
# Timestep Number-of-bins
# Bin Coord Ncount v_temp v_jx
100000 19
1 14.961 0 0 0
2 17.961 0 0 0
3 20.961 10 291.241 -0.00395033
"""
write(content, 'tmptestlinemanager.txt')
def getnscfin(self):
m = self.m
tmpl = self.getscf_template()
nscfk = self.getNscfKpoints()
aa = '\n'.join([m.toString(a) for a in nscfk])
newskpoints = "K_POINTS crystal\n%d\n%s" % (len(nscfk), aa)
s = tmpl.replace('TYPE',
'nscf').replace('CONTROL',
'').replace('KPOINTS', newskpoints)
tl.write(s, "nscf.in")
def getpedos(self):
tl.write("""&projwfc
outdir='./'
prefix='diam'
filpdos='diam.pedos',
Emin=-10.0, Emax=10.0, DeltaE=0.1,degauss=0.0025,ngauss=-99
/
""", "pedos.in")
projwfc = self.getx('projwfc')
tl.shell_exec(projwfc + " < pedos.in >pedos.out")
def get_fitin(self):
content = tl.read('alm.in').replace('suggest', 'fitting')
fitting = """&fitting
\tNDATA = %d
\tDFILE = disp_all.dat
\tFFILE = force_all.dat
/
""" % self.NDATA
fitting = tl.trimhead(fitting)
tl.write(content + fitting, 'fit.in')
def modulation(self):
m = self.m
conf = """
DIM = %s
MODULATION = 1 1 1, 0 0 0 0 1 0
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'modulation.conf')
passthru(config.phonopy + "--tolerance=1e-4 modulation.conf")
def force_constant(self, files):
cmd = config.phono3py + "--cf3 "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
tl.write(cmd, 'post.sh')
# generate FORCE_SETS
tl.passthru("sh post.sh")
m = self.m
print("Create fc2.hdf and fc3.hdf")
tl.passthru(config.phono3py + "-c POSCAR --dim='%s'" % (m.dim))
def modulation(self):
m = self.m
conf = """
DIM = %s
MODULATION = 1 1 1, 0 0 0 0 1 0
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'modulation.conf')
passthru(config.phonopy + "--tolerance=1e-4 modulation.conf")
def getpedos(self):
tl.write(
"""&projwfc
outdir='./'
prefix='diam'
filpdos='diam.pedos',
Emin=-10.0, Emax=10.0, DeltaE=0.1,degauss=0.0025,ngauss=-99
/
""", "pedos.in")
projwfc = self.getx('projwfc')
tl.shell_exec(projwfc + " < pedos.in >pedos.out")
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 getedos(self):
fermi = self.getfermi()
tl.write("""&DOS
outdir='./'
prefix='diam'
fildos='diam.edos',
Emin=%f, Emax=%f, DeltaE=0.01,degauss=0.005,ngauss=1
/
""" % (-4.0 + fermi, 4.0 + fermi), "edos.in")
dos = self.getx("dos")
tl.shell_exec(dos + " < edos.in >edos.out")
self.drawedos()
def animate(self):
m = self.m
conf = """
DIM = %s
ANIME = 0 5 20
ANIME_TYPE = xyz
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'animate.conf')
passthru(config.phonopy + "--tolerance=1e-4 animate.conf")
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 animate(self):
m = self.m
conf = """
DIM = %s
ANIME = 0 5 20
ANIME_TYPE = xyz
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'animate.conf')
passthru(config.phonopy + "--tolerance=1e-4 animate.conf")
def getdispforce(self, files):
force = ""
disp = ""
orig = io.read('POSCAR-supercell').positions
for dir0 in files:
forcearr = read_forces(
'dirs/dir_%s/vasprun.xml' % dir0) / 25.7110 # in Rd/bohr
force += matrixFormat(forcearr)
disparr = (io.read('dirs/dir_%s/POSCAR' % dir0).positions - orig
) * 1.889726 # in bohr
disp += matrixFormat(disparr)
tl.write(disp, "disp_all.dat")
tl.write(force, "force_all.dat")
def getdispforce(self, files):
force = ""
disp = ""
orig = io.read('POSCAR-supercell').positions
for dir0 in files:
forcearr = read_forces(
'dirs/dir_%s/vasprun.xml' % dir0) / 25.7110 # in Rd/bohr
force += matrixFormat(forcearr)
disparr = (io.read('dirs/dir_%s/POSCAR' % dir0).positions -
orig) * 1.889726 # in bohr
disp += matrixFormat(disparr)
tl.write(disp, "disp_all.dat")
tl.write(force, "force_all.dat")
def getedos(self):
fermi = self.getfermi()
tl.write(
"""&DOS
outdir='./'
prefix='diam'
fildos='diam.edos',
Emin=%f, Emax=%f, DeltaE=0.01,degauss=0.005,ngauss=1
/
""" % (-4.0 + fermi, 4.0 + fermi), "edos.in")
dos = self.getx("dos")
tl.shell_exec(dos + " < edos.in >edos.out")
self.drawedos()
def creatmini(self, m):
print('creatmini')
m.home = pwd()
assert m.home != ''
mkdir('minimize')
cd('minimize')
minimize_input(m)
write(time.strftime('%Y-%m-%d %H:%M:%S'), 'done')
cd('..')
if m.engine == "lammps":
return m.dump2POSCAR(m.home + '/minimize/range')
else:
return io.read(m.home + '/minimize/CONTCAR')
def getphin(self):
m = self.m
nqs = "nq1=%d,\n nq2= %d,\n nq3= %d," % tuple(m.kpoints)
s = """--
&inputph
prefix = 'diam'
fildyn = 'diam.dyn'
fildvscf = 'dvscf'
ldisp = .true
%s
tr2_ph = 1.0d-12
/
""" % nqs
tl.write(s, 'ph.in')
def getphin(self):
m = self.m
nqs = "nq1=%d,\n nq2= %d,\n nq3= %d," % tuple(m.kpoints)
s = """--
&inputph
prefix = 'diam'
fildyn = 'diam.dyn'
fildvscf = 'dvscf'
ldisp = .true
%s
tr2_ph = 1.0d-12
/
""" % nqs
tl.write(s, 'ph.in')
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 get_dos(self):
m = self.m
amass = self.get_amass()
nks = "nk1=%d,nk2= %d,nk3= %d" % tuple(m.nqf)
tl.write("""&input
asr='simple',
dos=.true.
%s
flfrc='diam.fc',
fldos='diam.dos',
%s
/""" % (amass, nks), "phdos.in")
matdyn = self.getx("matdyn", pa=False)
tl.shell_exec(matdyn + "< phdos.in >phdos.out")
self.drawDos()
def drawpr(self):
pr()
# plot
xs = []
ys = []
for line in open('pr.txt'):
x, y = map(float, line.split())
xs.append(x)
ys.append(y)
write("%s" % (sum(ys) / len(ys)), "ave_pr.txt")
with fig('Paticipation_ratio.png'):
pl.plot(xs, ys, '.', color='red')
pl.ylim([0.0, 1.0])
pl.xlabel('Frequency (THz)')
pl.ylabel('Paticipation Ratio')
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 drawpr(self):
pr()
# plot
xs = []
ys = []
for line in open('pr.txt'):
x, y = map(float, line.split())
xs.append(x)
ys.append(y)
write("%s" % (sum(ys) / len(ys)), "ave_pr.txt")
with fig('Paticipation_ratio.png'):
pl.plot(xs, ys, '.', color='red')
pl.ylim([0.0, 1.0])
pl.xlabel('Frequency (THz)')
pl.ylabel('Paticipation Ratio')
def get_dos(self):
m = self.m
amass = self.get_amass()
nks = "nk1=%d,nk2= %d,nk3= %d" % tuple(m.nqf)
tl.write(
"""&input
asr='simple',
dos=.true.
%s
flfrc='diam.fc',
fldos='diam.dos',
%s
/""" % (amass, nks), "phdos.in")
matdyn = self.getx("matdyn", pa=False)
tl.shell_exec(matdyn + "< phdos.in >phdos.out")
self.drawDos()
def get_almin(self):
m = self.m
m.atoms = io.read('POSCAR')
atoms = m.atoms.repeat(m.supercell)
general = """&general
\tPREFIX = alm
\tMODE = suggest
\tNAT = %s; NKD = %s
\tKD = %s
/
""" % (len(atoms), len(m.elements), m.toString(m.elements))
interaction = """&interaction
\tNORDER = 2
/
"""
cell = """&cell
\t1.889726
\t%s
/
""" % ('\n '.join([m.toString(atoms.cell[i]) for i in range(3)]))
cutoff = """&cutoff
\t*-* None %f
/
""" % (self.m.shengcut * 1.889726)
pos = ' \n'.join([
'\t%s ' % (m.elements.index(a.symbol) + 1) +
m.toString(atoms.get_scaled_positions()[i])
for i, a in enumerate(atoms)
])
position = """&position
%s
/
""" % pos
s = tl.headtrim(general + interaction + cell + cutoff + position)
tl.write(s, 'alm.in')
write_vasp('POSCAR-supercell',
atoms,
sort="True",
direct=True,
vasp5=True)
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 writeINCAR(self):
m = self.m
npar = 1
for i in range(1, int(np.sqrt(m.cores)) + 1):
if m.cores % i == 0:
npar = i
if m.ispin:
ispin = "ISPIN=2"
else:
ispin = ""
if m.soc:
soc = "LSORBIT=T"
else:
soc = ""
if m.isym:
sym = "ISYM = 1"
else:
sym = "ISYM = 0"
s = """SYSTEM=calculate energy
PREC = High
IBRION = -1
ENCUT = %f
EDIFF = 1.0e-8
ISMEAR = %d; SIGMA = 0.01
IALGO = 38
LREAL = .FALSE.
ADDGRID = .TRUE.
LWAVE = .FALSE.
LCHARG = .FALSE.
NPAR = %d
%s
%s
%s
""" % (self.m.ecut, m.ismear, npar, sym, ispin, soc)
if m.vdw:
s += """\nIVDW = 1
VDW_RADIUS = 50
VDW_S6 = 0.75
VDW_SR = 1.00
VDW_SCALING = 0.75
VDW_D = 20.0
VDW_C6 = 63.540 31.50
VDW_R0 = 1.898 1.892
"""
s = s.replace(r'^\s+', '')
write(s, 'INCAR')
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')
