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 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 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 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 generate(self):
m = self.m
coordination = self.phontsAtoms()
content0 = "species %d\n" % (len(m.elements)) + m.phontsmasses + """
D3_cutoff %f
kpoints %s 1
delta 0.005
numerical_2der T
numerical_3der T
iter_steps 3
pdos 0. 70. 200 10.
temp 60. 400. 10
AbInitio T F
FP_interface LAMMPS
#phonons_only T
Lattice 1.0
%s
end
""" % (m.shengcut, m.toString(m.kpoints), coordination)
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts) # generate many displacement files
tl.mkdir('lammps')
tl.cd('lammps')
content = "units %s\n" % m.units
content += """atom_style charge
dimension 3
boundary p p p
read_data GENERIC
%s
%s
neighbor 1.1 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 1 *.dump id fx fy fz
dump_modify 1 format "%%d %%30.20f %%30.20f %%30.20f"
dump_modify 1 sort id
run 0
""" % (m.masses, m.potential)
tl.shell_exec("mv ../*.str .")
strs = tl.shell_exec("ls *.str").split("\n")
for str in strs:
dir = str.replace("str", "dir")
tl.mkdir(dir)
tl.write(content.replace("GENERIC", str), dir + "/in")
tl.mv(str, "%s/%s" % (dir, str))
tl.cd(dir)
tl.passthru(config.lammps + " <in >out.dat")
tl.cd('..')
dirs = tl.shell_exec("ls |grep dir").split("\n")
for dir in dirs:
print(dir)
tl.cp(dir + "/0.dump", "../" + dir.replace("dir", "out"))
tl.cp("1.0000.dir/out.dat", "../1.0000.out")
tl.cd('..')
content0 = content0.replace('AbInitio T F', 'AbInitio F T')
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts)
def generate(self):
m = self.m
coordination = self.phontsAtoms()
content0 = "species %d\n" % (len(m.elements)) + m.phontsmasses + """
D3_cutoff %f
kpoints %s 1
delta 0.005
numerical_2der T
numerical_3der T
iter_steps 3
pdos 0. 70. 200 10.
temp 60. 400. 10
AbInitio T F
FP_interface LAMMPS
#phonons_only T
Lattice 1.0
%s
end
""" % (m.shengcut, m.toString(m.kpoints), coordination)
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts) # generate many displacement files
tl.mkdir('lammps')
tl.cd('lammps')
content = "units %s\n" % m.units
content += """atom_style charge
dimension 3
boundary p p p
read_data GENERIC
%s
%s
neighbor 1.1 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 1 *.dump id fx fy fz
dump_modify 1 format "%%d %%30.20f %%30.20f %%30.20f"
dump_modify 1 sort id
run 0
""" % (m.masses, m.potential)
tl.shell_exec("mv ../*.str .")
strs = tl.shell_exec("ls *.str").split("\n")
for str in strs:
dir = str.replace("str", "dir")
tl.mkdir(dir)
tl.write(content.replace("GENERIC", str), dir + "/in")
tl.mv(str, "%s/%s" % (dir, str))
tl.cd(dir)
tl.passthru(config.lammps + " <in >out.dat")
tl.cd('..')
dirs = tl.shell_exec("ls |grep dir").split("\n")
for dir in dirs:
print(dir)
tl.cp(dir + "/0.dump", "../" + dir.replace("dir", "out"))
tl.cp("1.0000.dir/out.dat", "../1.0000.out")
tl.cd('..')
content0 = content0.replace('AbInitio T F', 'AbInitio F T')
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts)
def run(self):
__console__ = sys.stdout
f = open('input', 'w', 0)
sys.stdout = f
self.generate()
sys.stdout = __console__
f.close()
cmd = self.runcmd()
shell_exec(cmd)
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 run0(self):
__console__ = sys.stdout
f = open('input', 'w', 0)
sys.stdout = f
self.generate()
sys.stdout = __console__
f.close()
cmd = self.runcmd()
shell_exec(cmd)
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 generate(self):
# self.minimizePOSCAR()
tl.shell_exec('cp minimize/POSCAR .')
self.get_almin()
self.displacements()
files, self.NDATA = self.getfiles()
self.getvasprun(files)
self.getdispforce(files)
self.get_fitin()
self.getfcs()
self.get_anphonin()
self.run_anphonin()
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 generate(self):
# self.minimizePOSCAR()
tl.shell_exec('cp minimize/POSCAR .')
self.get_almin()
self.displacements()
files, self.NDATA = self.getfiles()
self.getvasprun(files)
self.getdispforce(files)
self.get_fitin()
self.getfcs()
self.get_anphonin()
self.run_anphonin()
def getVaspRun_lammps(self):
m = self.m
if 'jm' in self.__dict__:
path = pwd()
pb = pbs(queue=m.queue,
nodes=1,
procs=4,
disp=m.pbsname,
path=path,
content=config.python + vasprun.__file__ + ' >log.out')
self.jm.reg(pb)
else:
shell_exec(config.python + vasprun.__file__ + ' >log.out')
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 collect(self):
tl.mkdir('save')
nqpt = len(tl.ls("diam.dyn*")) - 1
for iqpt in np.arange(1, nqpt + 1):
label = str(iqpt)
tl.shell_exec('cp diam.dyn' + str(iqpt) + ' save/diam.dyn_q' +
label)
if (iqpt == 1):
tl.shell_exec('cp _ph0/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('cp -r _ph0/diam.phsave save/')
else:
tl.shell_exec('cp _ph0/diam.q_' + str(iqpt) +
'/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('rm _ph0/diam.q_' + str(iqpt) + '/*wfc*')
def getVaspRun_lammps(self):
m = self.m
if 'jm' in self.__dict__:
path = pwd()
pb = pbs(
queue=m.queue,
nodes=1,
procs=4,
disp=m.pbsname,
path=path,
content=config.python + vasprun.__file__ + ' >log.out')
self.jm.reg(pb)
else:
shell_exec(config.python + vasprun.__file__ + ' >log.out')
def collect(self):
tl.mkdir('save')
nqpt = len(tl.ls("diam.dyn*")) - 1
for iqpt in np.arange(1, nqpt + 1):
label = str(iqpt)
tl.shell_exec('cp diam.dyn' + str(iqpt) + ' save/diam.dyn_q' +
label)
if (iqpt == 1):
tl.shell_exec('cp _ph0/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('cp -r _ph0/diam.phsave save/')
else:
tl.shell_exec('cp _ph0/diam.q_' + str(iqpt) +
'/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('rm _ph0/diam.q_' + str(iqpt) + '/*wfc*')
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 energyForce(self):
self.getVaspRun_vasp()
forces = parseVasprun('forces')
stress = parseVasprun('stress')
c = shell_exec("grep TOTEN OUTCAR|tail -1")
energy = sscanf(c, "free energy TOTEN = %f eV")[0]
return forces, stress, energy
def nAtom():
# atom number */
Natomline = tl.shell_exec("cd minimize;grep atoms log.out ;")
Natom = Natomline.split()[0]
if (Natom.isdigit() and Natom > 0):
return Natom
return 0
def kappa():
kappaline = tl.shell_exec("tail -1 result.txt 2>err;")
kappa = kappaline.split('=')
if len(kappa) > 1:
kappa = kappa[1]
return kappa
return 0.0
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 energyForce(self):
self.getVaspRun_vasp()
forces = parseVasprun('forces')
stress = parseVasprun('stress')
c = shell_exec("grep TOTEN OUTCAR|tail -1")
energy = sscanf(c, "free energy TOTEN = %f eV")[0]
return forces, stress, energy
def get_outfermi(self):
file = tl.ls("*.outputtrans")[0]
a = tl.shell_exec("grep FermiE %s|tail -1" % file)
from aces.scanf import sscanf
a = sscanf(a, "FermiE: %f.")[0]
print("E-fermi=" + str(a) + "Ry")
return a
def fc2(self):
files = shell_exec("ls dirs").split('\n')
files = map(lambda x: x.replace('dir_', ''), files)
# when the number of files >1000, the order is wrong ,POSCAR-001,
# POSCAR-1500 ,POSCAR-159
files.sort(lambda x, y: int(x.split('-')[1]) - int(y.split('-')[1]))
self.force_constant(files)
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 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 fc2(self):
files = shell_exec("ls dirs").split('\n')
files = map(lambda x: x.replace('dir_', ''), files)
# when the number of files >1000, the order is wrong ,POSCAR-001,
# POSCAR-1500 ,POSCAR-159
files.sort(lambda x, y: int(x.split('-')[1]) - int(y.split('-')[1]))
self.force_constant(files)
def run(self):
atoms = self.getsatoms()
symmetry = self.getSupercell(atoms)
files = tl.shell_exec(
'find dirs/dir_* -name vasprun.xml |sort -n').split('\n')
if len(files) > 100:
files = files[:100]
pos = atoms.positions
f, u = self.getForce(pos, files)
F, A = self.getCsMat(f, u, symmetry)
print("start compressive sensing ")
B = cs(mu=self.mu, split=self.split, lam=self.lam).run(F, A)
print("rebuilding IFCs ")
phi = self.rebuild(B)
print("writing IFCs ")
v = norm(u, axis=2)
u0 = v.flatten().max()
fc2 = np.einsum(phi[1], [1, 0, 3, 2]) / u0
writefc2(fc2, 'csfc2')
if self.NAH >= 3:
a = h5py.File('fc3p.hdf5')
if 'fc3' in a:
del a['fc3']
a['fc3'] = phi[2] / u0 / u0
a.close()
self.fc3()
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 kappa():
kappaline = tl.shell_exec("tail -1 result.txt 2>err;")
kappa = kappaline.split('=')
if len(kappa) > 1:
kappa = kappa[1]
return kappa
return 0.0
def testwritedata(self):
a=Atoms('C2',[[1,0,1],[0,1,1]])
a.set_cell([[1,0,1],[0,1,1],[0,0,1]])
d=lammpsdata(a,['C','N'])
d.writedata()
b=data('structure')
self.assertEqual(b.headers["atoms"],2)
self.assertEqual(b.headers["atom types"],2)
self.assertEqual(b.title ,'C2\n')
self.assertTrue(cc(b.headers["xlo xhi"],[0,sqrt(2)]))
self.assertTrue(cc(b.headers["ylo yhi"],[0,sqrt(2)*sqrt(3)/2]))
self.assertTrue(cc(b.headers["xy xz yz"][0:1],[sqrt(2)/2]))
b.map(1,'id',2,'type',3,'x',4,'y',5,'z')
atoms=b.viz(0)[2]
self.assertTrue(cc(atoms,[[1,1,sqrt(2),0,0],[2,1,sqrt(2)/2,sqrt(2)*sqrt(3)/2,0]]))
shell_exec('rm structure')
def nAtom():
# atom number */
Natomline = tl.shell_exec("cd minimize;grep atoms log.out ;")
Natom = Natomline.split()[0]
if(Natom.isdigit() and Natom > 0):
return Natom
return 0
def run(name):
path=home(name)
if not exists(path):
workdir=shell_exec('pwd')
cd(dirname(path))
passthru("make")
cd(workdir)
passthru(path)
def generate(self):
m = self.m
self.minimizePOSCAR()
a = time.time()
self.generate_supercells()
tl.debug('generate_supercells:%f s' % (time.time() - a))
tl.shell_exec("rm *-*")
tl.cp("SPOSCAR", "POSCAR001")
a = time.time()
files = ['POSCAR001']
self.getvasprun(files)
tl.debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.force_constant()
tl.debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def generate(self):
m = self.m
self.minimizePOSCAR()
a = time.time()
self.generate_supercells()
tl.debug('generate_supercells:%f s' % (time.time() - a))
tl.shell_exec("rm *-*")
tl.cp("SPOSCAR", "POSCAR001")
a = time.time()
files = ['POSCAR001']
self.getvasprun(files)
tl.debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.force_constant()
tl.debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def testwritedata(self):
a = Atoms('C2', [[1, 0, 1], [0, 1, 1]])
a.set_cell([[1, 0, 1], [0, 1, 1], [0, 0, 1]])
d = lammpsdata(a, ['C', 'N'])
d.writedata()
b = data('structure')
self.assertEqual(b.headers["atoms"], 2)
self.assertEqual(b.headers["atom types"], 2)
self.assertEqual(b.title, 'C2\n')
self.assertTrue(cc(b.headers["xlo xhi"], [0, sqrt(2)]))
self.assertTrue(cc(b.headers["ylo yhi"], [0, sqrt(2) * sqrt(3) / 2]))
self.assertTrue(cc(b.headers["xy xz yz"][0:1], [sqrt(2) / 2]))
b.map(1, 'id', 2, 'type', 3, 'x', 4, 'y', 5, 'z')
atoms = b.viz(0)[2]
self.assertTrue(
cc(atoms, [[1, 1, sqrt(2), 0, 0],
[2, 1, sqrt(2) / 2,
sqrt(2) * sqrt(3) / 2, 0]]))
shell_exec('rm structure')
def minimize_lammps(m):
f = open('input', 'w')
print >> f, "units %s" % m.units
print >> f, m.getatomicstyle()
print >> f, "boundary p p p"
print >> f, "dimension 3"
m.structure()
print >> f, 'read_data structure'
print >> f, m.potential
print >> f, "timestep %f" % m.timestep
print >> f, m.masses
print >> f, "thermo_style custom step pe etotal"
print >> f, "thermo %d" % m.dumpRate
if m.write_structure:
print >> f, "write_data structure"
print >> f, "dump dumpc all xyz 1CN.xyz"
print >> f, "run 0"
if m.metropolis:
print >> f, "min_style metropolis"
print >> f, "minimize 1e-12 1e-12 1000000 1000000"
if m.useMini:
if m.boxOpt:
if m.enforceThick:
print >> f, "fix 1 all box/relax x 0.0 y 0.0 nreset 1"
else:
print >> f, "fix 1 all box/relax iso 0.0 nreset 1"
print >> f, "min_style cg"
print >> f, "minimize 1e-12 1e-12 1000000 1000000"
print >> f, "write_restart restart.minimize"
print >> f, "dump dump1 all xyz 1 minimize.xyz"
print >> f, m.dump
print >> f, "dump kaka all atom 1 range"
print >> f, "dump_modify kaka sort id"
print >> f, "dump 1 all custom 1 dump.force id fx fy fz xs ys zs"
print >> f, "dump_modify 1 format \"%d %f %f %f %f %f %f\""
print >> f, "dump_modify 1 sort id"
print >> f, "run 0"
f.close()
tl.shell_exec(config.mpirun + " %s " % m.cores + config.lammps +
" <input >log.out")
m.postMini()
def get_band(self):
amass = self.get_amass()
m = self.m
rcell = m.atoms.get_reciprocal_cell().T
bp = m.bandpoints
kp = [rcell.dot(bp[x]) for x in m.bandpath]
bpath = [m.toString(x) for x in kp]
bs = '\t101\n'.join(bpath)
tl.write(
"""&input
asr='simple',
%s
flfrc='diam.fc',
flfrq='diam.freq',
q_in_band_form=.true.,
/
%d
%s 1""" % (amass, len(m.bandpath), bs), "band.in")
tl.shell_exec(config.espresso + "bin/matdyn.x < band.in >band.out")
self.get_bandplot()
a = np.loadtxt("band.plot")
c = np.unique(a[:, 0])
c = c[0:-1]
nqpoint = len(c)
s = "nqpoint: %d\n" % (nqpoint)
s += """npath: %d\n""" % (len(self.m.bandpath) - 1)
s += "phonon: \n"
for x in c:
filter = (a[:, 0] == x)
ys = a[filter, 1]
s += "- q-position: [ 0, 0.0000000, 0.0000000 ]\n"
s += " distance: %f\n" % x
s += " band:\n"
for i, y in enumerate(ys):
s += """ - # %d
frequency: %f\n""" % (i + 1, y / 33.367)
s += "\n"
tl.write(s, "band.yaml")
def generate(self):
m = self.m
self.minimizePOSCAR()
self.generate_supercells()
files = tl.shell_exec("ls *-*").split('\n')
self.getvasprun(files)
self.force_constant(files)
if m.pho3bte:
self.sheng()
else:
self.caltc()
self.dumpkappa()
def getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(
queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(
queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def get_band(self):
amass = self.get_amass()
m = self.m
rcell = m.atoms.get_reciprocal_cell().T
bp = m.bandpoints
kp = [rcell.dot(bp[x]) for x in m.bandpath]
bpath = [m.toString(x) for x in kp]
bs = '\t101\n'.join(bpath)
tl.write("""&input
asr='simple',
%s
flfrc='diam.fc',
flfrq='diam.freq',
q_in_band_form=.true.,
/
%d
%s 1""" % (amass, len(m.bandpath), bs), "band.in")
tl.shell_exec(config.espresso + "bin/matdyn.x < band.in >band.out")
self.get_bandplot()
a = np.loadtxt("band.plot")
c = np.unique(a[:, 0])
c = c[0:-1]
nqpoint = len(c)
s = "nqpoint: %d\n" % (nqpoint)
s += """npath: %d\n""" % (len(self.m.bandpath) - 1)
s += "phonon: \n"
for x in c:
filter = (a[:, 0] == x)
ys = a[filter, 1]
s += "- q-position: [ 0, 0.0000000, 0.0000000 ]\n"
s += " distance: %f\n" % x
s += " band:\n"
for i, y in enumerate(ys):
s += """ - # %d
frequency: %f\n""" % (i + 1, y / 33.367)
s += "\n"
tl.write(s, "band.yaml")
def clean(single):
if PROJHOME == '':
print("error PROJHOME")
# /*删除原始代码以外的文件*/
files = tl.shell_exec("cd %s;ls " % PROJHOME)
deleteFiles = []
files = files.split('\n')
for ls in files:
if (ls in ["sub.php", "post.php", "data", "", "sub.py"]):
continue
# print "deleting:%s"%ls;
deleteFiles.append(ls)
if len(deleteFiles) > 0:
print("All the files in " + str(deleteFiles) + " will be deleted.")
print("Comfirm ?[y/n]", end="")
sys.stdout.flush()
s = tl.input()
if (s != "y"):
tl.exit("exit with no change.")
comfirmStop(single)
for ls in deleteFiles:
tl.shell_exec("cd %s;rm -r %s" % (PROJHOME, ls))
def getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def tEnerty():
"""total energy
[description]
Returns:
[type] -- [description]
"""
totalEline = tl.shell_exec("cd minimize;tail -22 log.out| head -1;")
a = totalEline.split()
if(len(a) > 1):
totalE = [1]
return float(totalE)
return 0.0
def clean(single):
if PROJHOME == '':
print("error PROJHOME")
# /*删除原始代码以外的文件*/
files = tl.shell_exec("cd %s;ls " % PROJHOME)
deleteFiles = []
files = files.split('\n')
for ls in files:
if(ls in ["sub.php", "post.php", "data", "", "sub.py"]):
continue
# print "deleting:%s"%ls;
deleteFiles.append(ls)
if len(deleteFiles) > 0:
print("All the files in " + str(deleteFiles) +
" will be deleted.")
print("Comfirm ?[y/n]", end="")
sys.stdout.flush()
s = tl.input()
if(s != "y"):
tl.exit("exit with no change.")
comfirmStop(single)
for ls in deleteFiles:
tl.shell_exec("cd %s;rm -r %s" % (PROJHOME, ls))
def tEnerty():
"""total energy
[description]
Returns:
[type] -- [description]
"""
totalEline = tl.shell_exec("cd minimize;tail -22 log.out| head -1;")
a = totalEline.split()
if (len(a) > 1):
totalE = [1]
return float(totalE)
return 0.0
def getQueryInfo(workPath, pid, runTime):
pid = filter(str.isdigit, str(pid))
lastline = tl.shell_exec("tail -3 %s/log.out" % workPath)
qstat = tl.shell_exec("qstat %s 2>&1|tail -1 " % pid)
step = lastline.split()[0]
if step.isdigit():
percent = "%.1f%%" % (float(step) / runTime * 100)
else:
percent = "0"
if(qstat.find("Unknown Job Id") >= 0): # 该任务已从任务队列中去除*/
time = "complete"
if(lastline.find("builds") >= 0):
status = "C"
percent = "100%"
else: # 异常退出*/
status = "E"
else: # 正在运行或等待R&Q&C*/
time, status, queue = qstat.split()[3:6]
info = tl.shell_exec("qstat -f %s 2>&1|grep nodes" % pid)
info = info.split()[2]
return (percent, status)
def getQueryInfo(workPath, pid, runTime):
pid = filter(str.isdigit, str(pid))
lastline = tl.shell_exec("tail -3 %s/log.out" % workPath)
qstat = tl.shell_exec("qstat %s 2>&1|tail -1 " % pid)
step = lastline.split()[0]
if step.isdigit():
percent = "%.1f%%" % (float(step) / runTime * 100)
else:
percent = "0"
if (qstat.find("Unknown Job Id") >= 0): # 该任务已从任务队列中去除*/
time = "complete"
if (lastline.find("builds") >= 0):
status = "C"
percent = "100%"
else: # 异常退出*/
status = "E"
else: # 正在运行或等待R&Q&C*/
time, status, queue = qstat.split()[3:6]
info = tl.shell_exec("qstat -f %s 2>&1|grep nodes" % pid)
info = info.split()[2]
return (percent, status)
def tDisorder():
# disorder degree*/
now = tl.pwd()
tl.cd('minimize')
tl.mkcd('disorder')
disorderLine = tl.shell_exec(
"cp %s" % SRCHOME + "/in.disorder .;" + config.lammps +
" <in.disorder 2>err 1>log;tail -1 disorder.txt 2>err;")
k = disorderLine.split()[1:3]
if len(k) == 1:
k.append("")
disorder, rd = k
tl.cd(now)
return (disorder, rd)
def stub(self):
files = shell_exec("ls dirs").split('\n')
files = map(lambda x: x.replace('dir_', ''), files)
fc2 = readfc2('fc2')
for file in files:
ref = io.read('SPOSCAR')
a = 'dirs/dir_' + str(file)
atoms = io.read(a + "/POSCAR")
u = atoms.positions - ref.positions
f = -np.einsum('ijkl,jl', fc2, u)
forces = ""
for force in f:
forces += "<v> %f %f %f </v>\n" % tuple(force)
vasprun = '<root><calculation><varray name="forces" >\n'
vasprun += forces
vasprun += '</varray></calculation></root>\n'
write(vasprun, a + "/vasprun.xml")
def stub(self):
files = shell_exec("ls dirs").split('\n')
files = map(lambda x: x.replace('dir_', ''), files)
fc2 = readfc2('fc2')
for file in files:
ref = io.read('SPOSCAR')
a = 'dirs/dir_' + str(file)
atoms = io.read(a + "/POSCAR")
u = atoms.positions - ref.positions
f = -np.einsum('ijkl,jl', fc2, u)
forces = ""
for force in f:
forces += "<v> %f %f %f </v>\n" % tuple(force)
vasprun = '<root><calculation><varray name="forces" >\n'
vasprun += forces
vasprun += '</varray></calculation></root>\n'
write(vasprun, a + "/vasprun.xml")
def run(self):
m = self.m
a = time.time()
self.generate_supercells()
debug('generate_supercells:%f s' % (time.time() - a))
files = shell_exec("ls *-*").split('\n')
assert len(files) > 0 and not files[0] == ""
# self.runSPOSCAR()
a = time.time()
self.getvasprun(files)
debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.fc2()
debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def run(self):
m = self.m
a = time.time()
self.generate_supercells()
debug('generate_supercells:%f s' % (time.time() - a))
files = shell_exec("ls *-*").split('\n')
assert len(files) > 0 and not files[0] == ""
# self.runSPOSCAR()
a = time.time()
self.getvasprun(files)
debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.fc2()
debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
