def test_frames_from_structures(self):
"""Testing frames from structures."""
mgb2 = abidata.structure_from_ucell("MgB2")
sic = abidata.structure_from_ucell("SiC")
alas = abidata.structure_from_ucell("AlAs")
dfs = frames_from_structures([mgb2, sic, alas], index=None, with_spglib=True, cart_coords=False)
assert dfs.lattice is not None
assert dfs.coords is not None
assert dfs.structures is not None
formulas = [struct.composition.reduced_formula for struct in dfs.structures]
assert formulas == ["MgB2", "SiC", "AlAs"]
def test_dataframes_from_structures(self):
"""Testing dataframes from structures."""
mgb2 = abidata.structure_from_ucell("MgB2")
sic = abidata.structure_from_ucell("SiC")
alas = abidata.structure_from_ucell("AlAs")
dfs = dataframes_from_structures([mgb2, sic, alas], index=None, with_spglib=True, cart_coords=True)
dfs = dataframes_from_structures([mgb2, sic, alas], index=None, with_spglib=True, cart_coords=False)
assert dfs.lattice is not None
assert dfs.coords is not None
assert dfs.structures is not None
formulas = [struct.composition.reduced_formula for struct in dfs.structures]
assert formulas == ["MgB2", "SiC", "AlAs"]
def itest_phonon_restart(fwp):
"""Test the restart of phonon calculations with the scheduler."""
# Crystalline AlAs: computation of the second derivative of the total energy
structure = abidata.structure_from_ucell("AlAs")
# List of q-points for the phonon calculation (4,4,4) mesh.
qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
#5.00000000E-01, 0.00000000E+00, 0.00000000E+00, # XXX Uncomment this line to test restart from 1DEN
# Too long --> disabled
], (-1, 3))
# Global variables used both for the GS and the DFPT run.
global_vars = dict(
nband=4,
ecut=3.0,
ngkpt=[4, 4, 4],
shiftk=[0, 0, 0],
tolvrs=1.0e-5,
)
multi = abilab.MultiDataset(structure=structure, pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"),
ndtset=1 + len(qpoints))
multi.set_vars(global_vars)
for i, qpt in enumerate(qpoints):
# Response-function calculation for phonons.
multi[i+1].set_vars(
rfphon=1, # Will consider phonon-type perturbation.
nqpt=1, # One wavevector is to be considered.
qpt=qpt, # q-wavevector.
kptopt=3,
nstep=5, # This is to trigger the phonon restart.
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
# i == 0 --> restart from WFK
if i == 1: multi[i+1].set_vars(prtwf=-1, nstep=5) # Restart with WFK and smart- io.
if i == 2: multi[i+1].set_vars(prtwf=0, nstep=8) # Restart from 1DEN. Too long --> disabled.
all_inps = multi.split_datasets()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = flowtk.phonon_flow(fwp.workdir, scf_input, ph_inputs, manager=fwp.manager)
flow.set_garbage_collector()
for task in flow.iflat_tasks():
task.manager.qadapter.max_num_launches = 20
assert flow.make_scheduler().start() == 0
flow.check_status(show=True, verbose=1)
assert all(work.finalized for work in flow)
assert flow.all_ok
assert sum(task.num_restarts for task in flow.iflat_tasks()) > 0
def make_input(paral_kgb=1, paw=False):
"""Build a template input file for GS calculations with paral_kgb"""
pseudos = abidata.pseudos("14si.pspnc") if not paw else abidata.pseudos("Si.GGA_PBE-JTH-paw.xml")
inp = abilab.AbiInput(pseudos=pseudos)
inp.set_structure(abidata.structure_from_ucell("Si"))
inp.set_kmesh(ngkpt=[2,2,2], shiftk=[0,0,0])
# Global variables
ecut = 10
inp.set_vars(
ecut=ecut,
pawecutdg=ecut*4,
nsppol=1,
nband=20,
paral_kgb=paral_kgb,
npkpt=1,
npband=1,
npfft=1,
#
istwfk="*1",
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-10,
nstep=50,
)
return inp
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_","flow_")
flow = flowtk.Flow(options.workdir, manager=options.manager)
pseudos = abidata.pseudos("14si.pspnc")
# Get the unperturbed structure.
base_structure = abidata.structure_from_ucell("Si")
etas = [-.001, 0, +.001]
ph_displ = np.reshape(np.zeros(3*len(base_structure)), (-1,3))
ph_displ[0,:] = [+1, 0, 0]
ph_displ[1,:] = [-1, 0, 0]
# Build new structures by displacing atoms according to the phonon displacement
# ph_displ (in cartesian coordinates). The Displacement is normalized so that
# the maximum atomic diplacement is 1 Angstrom and then multiplied by eta.
modifier = abilab.StructureModifier(base_structure)
displaced_structures = modifier.displace(ph_displ, etas, frac_coords=False)
# Generate the different shifts to average
ndiv = 2
shift1D = np.arange(1,2*ndiv+1,2)/(2*ndiv)
all_shifts = [[x,y,z] for x in shift1D for y in shift1D for z in shift1D]
all_shifts = [[0, 0, 0]]
for structure, eta in zip(displaced_structures, etas):
for shift in all_shifts:
flow.register_work(raman_work(structure, pseudos, shift))
return flow
def make_scf_input(ecut=10, ngkpt=(8, 8, 8)):
"""
This function constructs an `AbinitInput` for performing a
GS-SCF calculation in crystalline AlAs.
Args:
ecut: cutoff energy in Ha.
ngkpt: 3 integers specifying the k-mesh for the electrons.
Return:
`AbinitInput` object
"""
# Initialize the AlAs structure from an internal database. Use the pseudos shipped with AbiPy.
gs_inp = abilab.AbinitInput(structure=abidata.structure_from_ucell("AlAs"),
pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"))
# Set the value of the Abinit variables needed for GS runs.
gs_inp.set_vars(
nband=4,
ecut=ecut,
ngkpt=ngkpt,
nshiftk=1,
shiftk=[0.0, 0.0, 0.0],
ixc=7,
nstep=500,
iscf=7,
diemac=5.0,
toldfe=1.0e-22,
nbdbuf=0,
kptopt=1,
)
gs_inp.set_mnemonics(True)
return gs_inp
def make_input(paw=False):
"""
Build and return an input file for GS calculations with paral_kgb=1
"""
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc")
#if not paw else
#abidata.pseudos("Si.GGA_PBE-JTH-paw.xml")
structure = abidata.structure_from_ucell("SiO2-alpha")
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[4, 4, 4], shiftk=[0,0,0.5])
# Global variables
ecut = 40
inp.set_vars(
ecut=ecut,
pawecutdg=ecut*4 if paw else None,
nsppol=1,
nband=32,
paral_kgb=1,
kptopt=3,
istwfk="*1",
timopt=-1,
chksymbreak=0,
nsym=1,
prtwf=0,
prtden=0,
tolvrs=1e-8,
nstep=20,
)
return inp
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
flow = flowtk.Flow(workdir=options.workdir)
scf_work = flowtk.Work()
ngkpt_list = [[4, 4, 4], [8, 8, 8], [12, 12, 12]]
tsmear_list = [0.01, 0.02, 0.04]
for ngkpt in ngkpt_list:
for tsmear in tsmear_list:
scf_input = make_scf_input(structure, ngkpt, tsmear, pseudos)
scf_work.register_scf_task(scf_input)
flow.register_work(scf_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [4, 4, 4] q-mesh.
for scf_task in scf_work:
ph_work = flowtk.PhononWork.from_scf_task(scf_task, qpoints=[4, 4, 4], is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def make_input(paw=False):
"""
Build and return an input file for GS calculations with paral_kgb=1
"""
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc") if not paw else \
abidata.pseudos("Si.GGA_PBE-JTH-paw.xml", "o.paw")
structure = abidata.structure_from_ucell("SiO2-alpha")
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[1, 1, 1], shiftk=[0, 0, 0])
# Global variables
ecut = 24
inp.set_vars(
ecut=ecut,
pawecutdg=ecut * 2 if paw else None,
paral_kgb=1,
nsppol=1,
nband=28,
npkpt=1,
npband=1,
npfft=1,
fftalg=112,
#istwfk="*1",
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-8,
nstep=10,
)
return inp
def get_gsinput_alas_ngkpt(ngkpt, usepaw=0, as_task=False):
"""
Build and return a GS input file for AlAs or a Task if `as_task`
"""
if usepaw != 0: raise NotImplementedError("PAW")
pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc")
structure = abidata.structure_from_ucell("AlAs")
from abipy.abio.inputs import AbinitInput
scf_input = AbinitInput(structure, pseudos=pseudos)
scf_input.set_vars(
nband=5,
ecut=8.0,
ngkpt=ngkpt,
nshiftk=1,
shiftk=[0, 0, 0],
tolvrs=1.0e-6,
diemac=12.0,
)
if not as_task:
return scf_input
else:
from abipy.flowtk.tasks import ScfTask
return ScfTask(scf_input)
def make_scf_nscf_inputs(nsppol):
inp = abilab.AbiInput(pseudos=data.pseudos("26fe.pspnc"), ndtset=2)
# Fe normal bcc structure for test of a ferromagnetic calculation
structure = data.structure_from_ucell("Fe-fm")
inp.set_structure(structure)
# Global variables
global_vars = dict(nsppol=nsppol,
ecut=18,
nband=8,
occopt=3,
tsmear=0.01,
)
if nsppol == 2:
global_vars.update(spinat=[0.0, 0.0, 4.0])
inp.set_variables(**global_vars)
# Dataset 1 (GS run)
inp[1].set_kmesh(ngkpt=[4,4,4], shiftk=[0.5,0.5,0.5])
inp[1].set_variables(tolvrs=1e-6)
# Dataset 2 (NSCF run)
inp[2].set_kpath(ndivsm=4)
inp[2].set_variables(tolwfr=1e-8)
# Generate two input files for the GS and the NSCF run
scf_input, nscf_input = inp.split_datasets()
return scf_input, nscf_input
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
flow = flowtk.Flow(workdir=options.workdir)
# Build work of GS task. Each gs_task uses different (ngkpt, tsmear) values
# and represent the starting point of the phonon works.
scf_work = flowtk.Work()
ngkpt_list = [[4, 4, 4], [8, 8, 8]] #, [12, 12, 12]]
tsmear_list = [0.01, 0.02] # , 0.04]
for ngkpt in ngkpt_list:
for tsmear in tsmear_list:
scf_input = make_scf_input(structure, ngkpt, tsmear, pseudos)
scf_work.register_scf_task(scf_input)
flow.register_work(scf_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [2, 2, 2] q-mesh.
# For each GS task, construct a phonon work that will inherit (ngkpt, tsmear) from scf_task.
for scf_task in scf_work:
ph_work = flowtk.PhononWork.from_scf_task(scf_task, qpoints=[2, 2, 2], is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def make_scf_input(ecut=10, ngkpt=(8, 8, 8)):
"""
This function constructs an `AbinitInput` for performing a
GS-SCF calculation in crystalline AlAs.
Args:
ecut: cutoff energy in Ha.
ngkpt: 3 integers specifying the k-mesh for the electrons.
Return:
`AbinitInput` object
"""
# Initialize the AlAs structure from an internal database. Use the pseudos shipped with AbiPy.
gs_inp = abilab.AbinitInput(structure=abidata.structure_from_ucell("AlAs"),
pseudos=abidata.pseudos(
"13al.981214.fhi", "33as.pspnc"))
# Set the value of the Abinit variables needed for GS runs.
gs_inp.set_vars(
nband=4,
ecut=ecut,
ngkpt=ngkpt,
nshiftk=1,
shiftk=[0.0, 0.0, 0.0],
ixc=7,
nstep=500,
iscf=7,
diemac=5.0,
toldfe=1.0e-22,
nbdbuf=0,
kptopt=1,
)
gs_inp.set_mnemonics(True)
return gs_inp
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(
".py", "").replace("run_", "flow_")
# Init structure from internal database.
structure = abidata.structure_from_ucell("MgB2")
# Our pseudopotentials.
pseudos = abilab.PseudoTable(["Mg-low.psp8", "B.psp8"])
flow = flowtk.Flow(workdir=options.workdir)
# Build work of GS task. Each gs_task uses different (ngkpt, tsmear) values
# and represent the starting point of the phonon works.
ngkpt = [12, 12, 12]
tsmear = 0.02
scf_input, nscf_input = make_scf_nscf_inputs(structure, ngkpt, tsmear,
pseudos)
gs_work = flowtk.Work()
scf_task = gs_work.register_scf_task(scf_input)
nscf_task = gs_work.register_nscf_task(nscf_input, deps={scf_task: "DEN"})
flow.register_work(gs_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [6, 6, 6] q-mesh.
ph_work = flowtk.PhononWork.from_scf_task(scf_task,
qpoints=[4, 4, 4],
is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def make_inputs(paral_kgb=1):
"""
Returns a tuple of 4 input files for SCF, NSCF, SCR, SIGMA calculations.
These files are then used as templates for the convergence study
wrt ecuteps and the number of bands in W.
"""
structure = abidata.structure_from_ucell("SiC")
pseudos = abidata.pseudos("14si.pspnc", "6c.pspnc")
ecut = 12
global_vars = dict(
ecut=ecut,
istwfk="*1",
paral_kgb=paral_kgb,
gwpara=2
)
ecuteps = 4
ngkpt = [4, 4, 4]
shiftk = [0, 0, 0]
inp = abilab.AbiInput(pseudos=pseudos, ndtset=4)
inp.set_structure(structure)
inp.set_vars(**global_vars)
inp.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
inp[1].set_vars(
nband=10,
tolvrs=1.e-8,
)
inp[2].set_vars(
nband=25,
tolwfr=1.e-8,
iscf=-2
)
inp[3].set_vars(
optdriver=3,
ecutwfn=ecut,
nband=20,
symchi=1,
inclvkb=0,
ecuteps=ecuteps,
)
inp[4].set_vars(
optdriver=4,
nband=20,
ecutwfn=ecut,
ecutsigx=ecut,
#ecutsigx=(4*ecut), ! This is problematic
symsigma=1,
ecuteps=ecuteps,
)
inp[4].set_kptgw(kptgw=[[0,0,0], [0.5, 0, 0]], bdgw=[1, 8])
return inp.split_datasets()
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
flow = abilab.Flow(workdir, manager=options.manager, remove=options.remove)
# Create the work for the band structure calculation.
structure = abidata.structure_from_ucell("NiO")
pseudos = abidata.pseudos("28ni.paw", "8o.2.paw")
# The code below set up the parameters for the LDA+U calculation in NiO.
#usepawu 1
#lpawu 2 -1
#upawu 8.0 0.0 eV
#jpawu 0.8 0.0 eV
usepawu = 1
u_values = [5.0, 8.0]
for u in u_values:
# Apply U-J on Ni only.
luj_params = abilab.LdauParams(usepawu, structure)
luj_params.luj_for_symbol("Ni", l=2, u=u, j=0.1*u, unit="eV")
scf_input, nscf_input, dos_input = make_scf_nscf_dos_inputs(structure, pseudos, luj_params)
work = abilab.BandStructureWork(scf_input, nscf_input, dos_inputs=dos_input)
flow.register_work(work)
return flow
def make_input(paw=False):
"""Build a template input file for GS calculations with k-point parallelism """
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc") if not paw else \
abidata.pseudos("Si.GGA_PBE-JTH-paw.xml", "o.paw")
structure = abidata.structure_from_ucell("SiO2-alpha")
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[1,1,1], shiftk=[0,0,0])
# Global variables
ecut = 24
inp.set_vars(
ecut=ecut,
pawecutdg=ecut*2 if paw else None,
nsppol=1,
nband=28,
paral_kgb=0,
#istwfk="*1",
#fftalg=312,
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-10,
)
return inp
def make_input():
"""Build a template input file for GS calculations with k-point parallelism """
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc")
structure = abidata.structure_from_ucell("SiO2-alpha")
#structure.make_supercell([3,3,3])
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[4, 4, 4], shiftk=[0, 0, 0])
# Global variables
ecut = 24
inp.set_vars(
ecut=ecut,
nsppol=1,
nband=28,
paral_kgb=0,
istwfk="*1",
timopt=-1,
chksymbreak=0,
chkprim=0,
maxnsym=2400,
prtwf=0,
prtden=0,
tolvrs=1e-8,
)
return inp
def make_scf_nscf_inputs(nsppol, paral_kgb=1):
"""
Generate two input files for the GS and the NSCF run for given `nsppol`.
"""
# Fe normal bcc structure for test of a ferromagnetic calculation
multi = abilab.MultiDataset(structure=data.structure_from_ucell("Fe-fm"),
pseudos=data.pseudos("26fe.pspnc"), ndtset=2)
# Global variables
global_vars = dict(
nsppol=nsppol,
ecut=18,
nband=8,
occopt=3,
tsmear=0.01,
paral_kgb=paral_kgb,
)
if nsppol == 2:
global_vars.update(spinat=[0.0, 0.0, 4.0])
multi.set_vars(global_vars)
# Dataset 1 (GS run)
multi[0].set_kmesh(ngkpt=[4,4,4], shiftk=[0.5,0.5,0.5])
multi[0].set_vars(tolvrs=1e-6)
# Dataset 2 (NSCF run)
multi[1].set_kpath(ndivsm=4)
multi[1].set_vars(tolwfr=1e-8)
# Generate two input files for the GS and the NSCF run
scf_input, nscf_input = multi.split_datasets()
return scf_input, nscf_input
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
flow = abilab.Flow(workdir, manager=options.manager)
# Create the work for the band structure calculation.
structure = abidata.structure_from_ucell("NiO")
pseudos = abidata.pseudos("28ni.paw", "8o.2.paw")
# The code below set up the parameters for the LDA+U calculation in NiO.
#usepawu 1
#lpawu 2 -1
#upawu 8.0 0.0 eV
#jpawu 0.8 0.0 eV
usepawu = 1
u_values = [5.0, 8.0]
for u in u_values:
# Apply U-J on Ni only.
luj_params = abilab.LdauParams(usepawu, structure)
luj_params.luj_for_symbol("Ni", l=2, u=u, j=0.1*u, unit="eV")
scf_input, nscf_input, dos_input = make_scf_nscf_dos_inputs(structure, pseudos, luj_params)
work = abilab.BandStructureWork(scf_input, nscf_input, dos_inputs=dos_input)
flow.register_work(work)
return flow
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(
".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
flow = flowtk.Flow(workdir=options.workdir)
# Build work of GS task. Each gs_task uses different (ngkpt, tsmear) values
# and represent the starting point of the phonon works.
scf_work = flowtk.Work()
ngkpt_list = [[4, 4, 4], [8, 8, 8]] #, [12, 12, 12]]
tsmear_list = [0.01, 0.02] # , 0.04]
for ngkpt in ngkpt_list:
for tsmear in tsmear_list:
scf_input = make_scf_input(structure, ngkpt, tsmear, pseudos)
scf_work.register_scf_task(scf_input)
flow.register_work(scf_work)
# This call uses the information reported in the GS task to
# compute all the independent atomic perturbations corresponding to a [2, 2, 2] q-mesh.
# For each GS task, construct a phonon work that will inherit (ngkpt, tsmear) from scf_task.
for scf_task in scf_work:
ph_work = flowtk.PhononWork.from_scf_task(scf_task,
qpoints=[2, 2, 2],
is_ngqpt=True)
flow.register_work(ph_work)
return flow.allocate(use_smartio=True)
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
flow = flowtk.Flow(options.workdir, manager=options.manager)
pseudos = abidata.pseudos("14si.pspnc")
# Get the unperturbed structure.
base_structure = abidata.structure_from_ucell("Si")
etas = [-.001, 0, +.001]
ph_displ = np.reshape(np.zeros(3*len(base_structure)), (-1,3))
ph_displ[0,:] = [+1, 0, 0]
ph_displ[1,:] = [-1, 0, 0]
# Build new structures by displacing atoms according to the phonon displacement
# ph_displ (in cartesian coordinates). The Displacement is normalized so that
# the maximum atomic diplacement is 1 Angstrom and then multiplied by eta.
modifier = abilab.StructureModifier(base_structure)
displaced_structures = modifier.displace(ph_displ, etas, frac_coords=False)
# Generate the different shifts to average
ndiv = 2
shift1D = np.arange(1,2*ndiv+1,2)/(2*ndiv)
all_shifts = [[x,y,z] for x in shift1D for y in shift1D for z in shift1D]
all_shifts = [[0, 0, 0]]
for structure, eta in zip(displaced_structures, etas):
for shift in all_shifts:
flow.register_work(raman_work(structure, pseudos, shift))
return flow
def make_input(paw=False):
"""Build a template for GS calculations with k-point parallelism"""
pseudos = abidata.pseudos("14si.pspnc") if not paw else abidata.pseudos(
"Si.GGA_PBE-JTH-paw.xml")
structure = abidata.structure_from_ucell("Si")
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[12, 12, 12], shiftk=[0, 0, 0])
# Global variables
ecut = 40
inp.set_vars(
ecut=ecut,
pawecutdg=ecut * 4 if paw else None,
nsppol=2,
nband=40,
paral_kgb=0,
#istwfk="*1",
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-10,
)
return inp
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
#pseudos = abidata.pseudos("12mg.pspnc", "5b.pspnc")
structure = abidata.structure_from_ucell("MgB2")
# Get pseudos from a table.
table = abilab.PseudoTable(abidata.pseudos("12mg.pspnc", "5b.pspnc"))
pseudos = table.get_pseudos_for_structure(structure)
nval = structure.num_valence_electrons(pseudos)
#print(nval)
inputs = make_scf_nscf_inputs(structure, pseudos)
scf_input, nscf_input, dos_inputs = inputs[0], inputs[1], inputs[2:]
#print(scf_input.pseudos)
return abilab.bandstructure_flow(workdir,
scf_input,
nscf_input,
dos_inputs=dos_inputs,
manager=options.manager)
def make_scf_nscf_inputs(nsppol, paral_kgb=1):
"""
Generate two input files for the GS and the NSCF run for given `nsppol`.
"""
# Fe normal bcc structure for test of a ferromagnetic calculation
multi = abilab.MultiDataset(structure=data.structure_from_ucell("Fe-fm"),
pseudos=data.pseudos("26fe.pspnc"), ndtset=2)
# Global variables
global_vars = dict(
nsppol=nsppol,
ecut=18,
nband=8,
occopt=3,
tsmear=0.01,
paral_kgb=paral_kgb,
)
if nsppol == 2:
global_vars.update(spinat=[0.0, 0.0, 4.0])
multi.set_vars(global_vars)
# Dataset 1 (GS run)
multi[0].set_kmesh(ngkpt=[4,4,4], shiftk=[0.5,0.5,0.5])
multi[0].set_vars(tolvrs=1e-6)
# Dataset 2 (NSCF run)
multi[1].set_kpath(ndivsm=4)
multi[1].set_vars(tolwfr=1e-8)
# Generate two input files for the GS and the NSCF run
scf_input, nscf_input = multi.split_datasets()
return scf_input, nscf_input
def make_input():
"""Build a template input file for GS calculations with k-point parallelism """
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc")
structure = abidata.structure_from_ucell("SiO2-alpha")
#structure.make_supercell([3,3,3])
inp = abilab.AbinitInput(structure, pseudos)
inp.set_kmesh(ngkpt=[4,4,4], shiftk=[0,0,0])
# Global variables
ecut = 24
inp.set_vars(
ecut=ecut,
nsppol=1,
nband=28,
paral_kgb=0,
istwfk="*1",
timopt=-1,
chksymbreak=0,
chkprim=0,
maxnsym=2400,
prtwf=0,
prtden=0,
tolvrs=1e-8,
)
return inp
def make_inputs(paral_kgb=1):
"""
Returns a tuple of 4 input files for SCF, NSCF, SCR, SIGMA calculations.
These files are then used as templates for the convergence study
wrt ecuteps and the number of bands in W.
"""
multi = abilab.MultiDataset(abidata.structure_from_ucell("SiC"),
pseudos=abidata.pseudos(
"14si.pspnc", "6c.pspnc"),
ndtset=4)
ecut = 12
global_vars = dict(
ecut=ecut,
istwfk="*1",
paral_kgb=paral_kgb,
gwpara=2,
iomode=1,
)
ecuteps = 4
ngkpt = [4, 4, 4]
shiftk = [0, 0, 0]
multi.set_vars(global_vars)
multi.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
# SCF
multi[0].set_vars(
nband=10,
tolvrs=1.e-8,
)
# NSCF
multi[1].set_vars(nband=25, tolwfr=1.e-8, iscf=-2)
# SCR
multi[2].set_vars(
optdriver=3,
ecutwfn=ecut,
nband=20,
symchi=1,
inclvkb=0,
ecuteps=ecuteps,
)
# SIGMA
multi[3].set_vars(
optdriver=4,
nband=20,
ecutwfn=ecut,
ecutsigx=ecut,
#ecutsigx=(4*ecut), ! This is problematic
symsigma=1,
ecuteps=ecuteps,
)
multi[3].set_kptgw(kptgw=[[0, 0, 0], [0.5, 0, 0]], bdgw=[1, 8])
return multi.split_datasets()
def test_base(self):
"""Testing ScalarField."""
structure = abidata.structure_from_ucell("Si")
nspinor, nsppol, nspden = 1, 1, 1
xyz_shape = (2, 3, 4)
datar = np.zeros((nsppol, ) + xyz_shape)
field = ScalarField(nspinor,
nsppol,
nspden,
datar,
structure,
iorder="c")
print(field)
assert field.datar.ndim == 4
assert len(field) == nsppol
assert field.shape == datar.shape
assert field.nx == 2 and field.ny == 3 and field.nz == 4
assert field.is_collinear
#assert field.datar_xyz.ndim == 4
#assert field.datar_xyz.shape[-3:], xyz_shape)
field.export(self.get_tmpname(text=True, suffix=".xsf"))
def make_template():
"""Build a template input file for GS calculations with paral_kgb"""
inp = abilab.AbiInput(pseudos=data.pseudos("14si.pspnc"))
inp.set_structure(data.structure_from_ucell("Si"))
# GS run with paral_kgb
inp.set_kmesh(ngkpt=[1,1,1], shiftk=[0,0,0])
# Global variables
global_vars = dict(ecut=20,
nsppol=1,
nband=20,
paral_kgb=1,
npkpt=1,
npband=1,
npfft=1,
#
istwfk="*1",
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-8,
nstep=10,
)
inp.set_variables(**global_vars)
return inp
def make_scf_input(ecut=2, ngkpt=(4, 4, 4)):
"""
This function constructs an `AbinitInput` for performing a
GS-SCF calculation in crystalline AlAs.
Args:
ecut: cutoff energy in Ha.
ngkpt: 3 integers specifying the k-mesh for the electrons.
Return:
`AbinitInput` object
"""
# Initialize the AlAs structure from an internal database. Use the pseudos shipped with AbiPy.
gs_inp = abilab.AbinitInput(structure=abidata.structure_from_ucell("AlAs"),
pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"))
# Set the value of the Abinit variables needed for GS runs.
gs_inp.set_vars(
nband=4,
ecut=ecut,
ngkpt=ngkpt,
nshiftk=4,
shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid
0.0, 0.5, 0.0,
0.5, 0.0, 0.0,
0.5, 0.5, 0.5],
ixc=1,
nstep=25,
diemac=9.0,
tolvrs=1.0e-10,
)
gs_inp.set_mnemonics(True)
return gs_inp
def make_template(paral_kgb=1, paw=False):
"""Build a template input file for GS calculations with paral_kgb"""
pseudos = abidata.pseudos("14si.pspnc") if not paw else abidata.pseudos(
"Si.GGA_PBE-JTH-paw.xml")
inp = abilab.AbiInput(pseudos=pseudos, ndtset=1)
inp.set_structure(abidata.structure_from_ucell("Si"))
# GS run with paral_kgb
inp.set_kmesh(ngkpt=[1, 1, 1], shiftk=[0, 0, 0])
# Global variables
ecut = 20
global_vars = dict(
ecut=ecut,
pawecutdg=ecut * 4,
nsppol=1,
nband=20,
paral_kgb=paral_kgb,
npkpt=1,
npband=1,
npfft=1,
fftalg=112,
#
istwfk="*1",
timopt=-1,
chksymbreak=0,
prtwf=0,
prtden=0,
tolvrs=1e-8,
nstep=10,
)
inp.set_variables(**global_vars)
return inp
def make_scf_input(paral_kgb=0):
"""
This function constructs the input files for the phonon calculation:
GS input + the input files for the phonon calculation.
"""
# Crystalline AlAs: computation of the second derivative of the total energy
structure = abidata.structure_from_ucell("AlAs")
pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc")
gs_inp = abilab.AbinitInput(structure, pseudos=pseudos)
gs_inp.set_vars(
nband=4,
ecut=2.0,
ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid
0.0, 0.5, 0.0,
0.5, 0.0, 0.0,
0.5, 0.5, 0.5],
#shiftk=[0, 0, 0],
paral_kgb=paral_kgb,
tolvrs=1.0e-10,
ixc=1,
diemac=9.0,
iomode=3,
)
return gs_inp
def make_inputs(tvars):
"""Constrcut the input files."""
structure = abidata.structure_from_ucell("GaAs")
inp = abilab.AbiInput(pseudos=abidata.pseudos("31ga.pspnc", "33as.pspnc"), ndtset=5)
inp.set_structure(structure)
# Global variables
kmesh = dict(ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
global_vars = dict(ecut=2,
paral_kgb=tvars.paral_kgb)
global_vars.update(kmesh)
inp.set_variables(**global_vars)
# Dataset 1 (GS run)
inp[1].set_variables(
tolvrs=1e-6,
nband=4)
# NSCF run with large number of bands, and points in the the full BZ
inp[2].set_variables(
iscf=-2,
nband=20,
nstep=25,
kptopt=1,
tolwfr=1.e-8)
#kptopt=3)
# Fourth dataset: ddk response function along axis 1
# Fifth dataset: ddk response function along axis 2
# Sixth dataset: ddk response function along axis 3
for idir in range(3):
rfdir = 3 * [0]
rfdir[idir] = 1
inp[3+idir].set_variables(
iscf=-3,
nband=20,
nstep=1,
nline=0,
prtwf=3,
kptopt=3,
nqpt=1,
qpt=[0.0, 0.0, 0.0],
rfdir=rfdir,
rfelfd=2,
tolwfr=1.e-9,
)
# scf_inp, nscf_inp, ddk1, ddk2, ddk3
return inp.split_datasets()
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace("run_","flow_")
# Instantiate the TaskManager.
manager = abilab.TaskManager.from_user_config() if not options.manager else \
abilab.TaskManager.from_file(options.manager)
flow = abilab.Flow(workdir, manager)
pseudos = data.pseudos("14si.pspnc", "6c.pspnc")
structure = data.structure_from_ucell("SiC")
global_vars = dict(
chksymbreak=0,
ecut=20,
paral_kgb=0,
)
ngkpt = [4,4,4]
shiftk = [[0.5,0.5,0.5],
[0.5,0.0,0.0],
[0.0,0.5,0.0],
[0.0,0.0,0.5]]
inp = abilab.AbiInput(pseudos=pseudos, ndtset=2)
inp.set_structure(structure)
inp.set_vars(**global_vars)
relax_inp, nscf_inp = inp[1:]
relax_inp.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
relax_inp.set_vars(
toldff=1e-6,
tolmxf=1e-5,
strfact=100,
ecutsm=0.5,
dilatmx=1.15,
ntime=100,
ionmov=2,
optcell=1,
)
nscf_inp.set_kpath(ndivsm=20)
nscf_inp.tolwfr = 1e-22
relax_inp, nscf_inp = inp.split_datasets()
# Initialize the work.
relax_task = flow.register_task(relax_inp, task_class=abilab.RelaxTask)
#work = RelaxWork(self, ion_input, ioncell_input, workdir=None, manager=None):
nscf_task = flow.register_task(nscf_inp, deps={relax_task: "DEN"}, task_class=abilab.NscfTask)
return flow.allocate()
def itest_phonon_restart(fwp):
"""Test the restart of phonon calculations with the scheduler."""
# Crystalline AlAs: computation of the second derivative of the total energy
structure = abidata.structure_from_ucell("AlAs")
# List of q-points for the phonon calculation (4,4,4) mesh.
qpoints = np.reshape([
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
#5.00000000E-01, 0.00000000E+00, 0.00000000E+00, # XXX Uncomment this line to test restart from 1DEN
# Too long --> disabled
], (-1, 3))
# Global variables used both for the GS and the DFPT run.
global_vars = dict(nband=4,
ecut=3.0,
ngkpt=[4, 4, 4],
shiftk=[0, 0, 0],
tolvrs=1.0e-5,
)
multi = abilab.MultiDataset(structure=structure, pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"),
ndtset=1+len(qpoints))
multi.set_vars(global_vars)
for i, qpt in enumerate(qpoints):
# Response-function calculation for phonons.
multi[i+1].set_vars(
rfphon=1, # Will consider phonon-type perturbation.
nqpt=1, # One wavevector is to be considered.
qpt=qpt, # q-wavevector.
kptopt=3,
nstep=5, # This is to trigger the phonon restart.
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
# i == 0 --> restart from WFK
if i == 1: multi[i+1].set_vars(prtwf=-1, nstep=5) # Restart with WFK and smart- io.
if i == 2: multi[i+1].set_vars(prtwf=0, nstep=8) # Restart from 1DEN. Too long --> disabled.
all_inps = multi.split_datasets()
scf_input, ph_inputs = all_inps[0], all_inps[1:]
flow = abilab.phonon_flow(fwp.workdir, scf_input, ph_inputs, manager=fwp.manager)
flow.set_garbage_collector()
for task in flow.iflat_tasks():
task.manager.qadapter.max_num_launches = 20
assert flow.make_scheduler().start() == 0
flow.check_status(show=True, verbose=1)
assert all(work.finalized for work in flow)
assert flow.all_ok
assert sum(task.num_restarts for task in flow.iflat_tasks()) > 0
def make_inputs(paw=False):
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc") if not paw else \
abidata.pseudos("Si.GGA_PBE-JTH-paw.xml", "o.paw")
structure = abidata.structure_from_ucell("SiO2-alpha")
multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=4)
ecut = 24
multi.set_vars(
ecut=ecut,
pawecutdg=ecut * 2 if paw else None,
paral_kgb=0,
istwfk="*1",
timopt=-1,
)
multi.set_kmesh(ngkpt=[4, 4, 3], shiftk=[0.0, 0.0, 0.0])
gs, nscf, scr, sigma = multi.split_datasets()
# Dataset 1 (GS run)
gs.set_vars(
tolvrs=1e-6,
nband=28,
)
# Dataset 2 (NSCF run)
nscf.set_vars(
iscf=-2,
tolwfr=1e-4,
nband=600,
nbdbuf=200,
)
# Dataset3: Calculation of the screening.
scr.set_vars(
optdriver=3,
gwpara=2,
nband=25,
ecutwfn=ecut,
symchi=1,
inclvkb=0,
ecuteps=6.0,
)
# Dataset4: Calculation of the Self-Energy matrix elements (GW corrections)
sigma.set_vars(
optdriver=4,
gwpara=2,
ecutwfn=ecut,
ecuteps=6.0,
ecutsigx=ecut,
symsigma=1,
gw_qprange=1,
)
return gs, nscf, scr, sigma
def build_flow(options):
# Set working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("GaAs")
pseudos = abidata.pseudos("Ga-low_r.psp8", "As_r.psp8")
num_electrons = structure.num_valence_electrons(pseudos)
#print("num_electrons:", num_electrons)
# Usa same shifts in all tasks.
ngkpt = [4, 4, 4]
shiftk= [
[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5],
]
# NSCF run on k-path with large number of bands
kptbounds = [
[0.5, 0.0, 0.0], # L point
[0.0, 0.0, 0.0], # Gamma point
[0.0, 0.5, 0.5], # X point
]
# Initialize the flow.
flow = flowtk.Flow(options.workdir, manager=options.manager)
for nspinor in [1, 2]:
# Multi will contain two datasets (GS + NSCF) for the given nspinor.
multi = abilab.MultiDataset(structure=structure, pseudos=pseudos, ndtset=2)
# Global variables.
multi.set_vars(
ecut=20,
nspinor=nspinor,
nspden=1 if nspinor == 1 else 4,
so_psp="*0" if nspinor == 1 else "*1", # Important!
#paral_kgb=1,
)
nband_occ = num_electrons // 2 if nspinor == 1 else num_electrons
#print(nband_occ)
# Dataset 1 (GS run)
multi[0].set_vars(tolvrs=1e-8, nband=nband_occ + 4)
multi[0].set_kmesh(ngkpt=ngkpt, shiftk=shiftk, kptopt=1 if nspinor == 1 else 4)
multi[1].set_vars(iscf=-2, nband=nband_occ + 4, tolwfr=1.e-12)
multi[1].set_kpath(ndivsm=10, kptbounds=kptbounds)
# Get the SCF and the NSCF input.
scf_input, nscf_input = multi.split_datasets()
flow.register_work(flowtk.BandStructureWork(scf_input, nscf_input))
return flow
def build_flow(options):
# Set working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(sys.argv[0]).replace(".py", "").replace("run_", "flow_")
structure = abidata.structure_from_ucell("GaAs")
pseudos = abidata.pseudos("Ga-low_r.psp8", "As_r.psp8")
num_electrons = structure.num_valence_electrons(pseudos)
#print("num_electrons:", num_electrons)
# Usa same shifts in all tasks.
ngkpt = [4, 4, 4]
shiftk = [
[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5],
]
# NSCF run on k-path with large number of bands
kptbounds = [
[0.5, 0.0, 0.0], # L point
[0.0, 0.0, 0.0], # Gamma point
[0.0, 0.5, 0.5], # X point
]
# Initialize the flow.
flow = flowtk.Flow(options.workdir, manager=options.manager)
for nspinor in [1, 2]:
# Multi will contain two datasets (GS + NSCF) for the given nspinor.
multi = abilab.MultiDataset(structure=structure, pseudos=pseudos, ndtset=2)
# Global variables.
multi.set_vars(
ecut=20,
nspinor=nspinor,
nspden=1 if nspinor == 1 else 4,
so_psp="*0" if nspinor == 1 else "*1", # Important!
#paral_kgb=1,
)
nband_occ = num_electrons // 2 if nspinor == 1 else num_electrons
#print(nband_occ)
# Dataset 1 (GS run)
multi[0].set_vars(tolvrs=1e-8, nband=nband_occ + 4)
multi[0].set_kmesh(ngkpt=ngkpt, shiftk=shiftk, kptopt=1 if nspinor == 1 else 4)
multi[1].set_vars(iscf=-2, nband=nband_occ + 4, tolwfr=1.e-12)
multi[1].set_kpath(ndivsm=10, kptbounds=kptbounds)
# Get the SCF and the NSCF input.
scf_input, nscf_input = multi.split_datasets()
flow.register_work(flowtk.BandStructureWork(scf_input, nscf_input))
return flow
def test_utils(self):
"""Test utilities for the generation of Abinit inputs."""
# Test as_structure and from/to abivars
si = Structure.as_structure(abidata.cif_file("si.cif"))
assert si.formula == "Si2"
assert si.abi_spacegroup is None and not si.has_abi_spacegroup
if self.has_matplotlib():
si.show_bz(show=False)
assert si is Structure.as_structure(si)
assert si == Structure.as_structure(si.to_abivars())
assert si == Structure.from_abivars(si.to_abivars())
assert len(si.abi_string)
assert si.reciprocal_lattice == si.lattice.reciprocal_lattice
#si.si_kptbounds()
#si.calc_ksampling(nksmall=10)
#si.calc_ngkpt(nksmall=10)
#si.calc_shiftk()
si = Structure.from_material_id("mp-149", api_key="8pkvwRLQSCVbW2Fe")
assert si.formula == "Si2"
mgb2 = abidata.structure_from_ucell("MgB2")
if self.has_ase():
mgb2.abi_primitive()
# FIXME: This is buggy
#print(mgb2.get_sorted_mgb2())
#assert [site.species_string for site in mgb2.get_sorted_structure()] == ["B", "B", "Mg"]
mgb2.abi_sanitize()
mgb2.get_conventional_standard_structure()
assert len(mgb2.abi_string)
assert len(mgb2.spglib_summary(verbose=10))
#print(structure.__repr_html__())
self.serialize_with_pickle(mgb2)
pseudos = abidata.pseudos("12mg.pspnc", "5b.pspnc")
assert mgb2.num_valence_electrons(pseudos) == 8
assert mgb2.valence_electrons_per_atom(pseudos) == [2, 3, 3]
self.assert_equal(mgb2.calc_shiftk() , [[0.0, 0.0, 0.5]])
#bmol = Structure.boxed_molecule(pseudos, cart_coords=[[0, 0, 0], [5, 5, 5]])
#self.assert_almost_equal(bmol.volume, (10 * bohr_to_ang) ** 3)
#batom = Structure.boxed_atom(abidata.pseudo("12mg.pspnc"), cart_coords=[1, 2, 3], acell=(10, 20, 30))
#assert isinstance(batom, Structure)
#assert len(batom.cart_coords) == 1 and np.all(batom.cart_coords[0] == [1, 2, 3])
#bcc = Structure.bcc(a=10, species, primitive)
#fcc = Structure.bcc(a=10, species, primitive)
#rock = Structure.rocksalt(a=10, species)
#perov = Structure.ABO3(a=10, species)
# Test notebook generation.
if self.has_nbformat():
mgb2.write_notebook(nbpath=self.get_tmpname(text=True))
def make_inputs(paw=False):
pseudos = abidata.pseudos("14si.pspnc", "8o.pspnc") if not paw else \
abidata.pseudos("Si.GGA_PBE-JTH-paw.xml", "o.paw")
structure = abidata.structure_from_ucell("SiO2-alpha")
multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=4)
ecut = 24
multi.set_vars(
ecut=ecut,
pawecutdg=ecut*2 if paw else None,
paral_kgb=0,
istwfk="*1",
timopt=-1,
)
multi.set_kmesh(ngkpt=[4,4,3], shiftk=[0.0, 0.0, 0.0])
gs, nscf, scr, sigma = multi.split_datasets()
# Dataset 1 (GS run)
gs.set_vars(tolvrs=1e-6,
nband=28,)
# Dataset 2 (NSCF run)
nscf.set_vars(iscf=-2,
tolwfr=1e-4,
nband=600,
nbdbuf=200,
)
# Dataset3: Calculation of the screening.
scr.set_vars(
optdriver=3,
gwpara=2,
nband=25,
ecutwfn=ecut,
symchi=1,
inclvkb=0,
ecuteps=6.0,
)
# Dataset4: Calculation of the Self-Energy matrix elements (GW corrections)
sigma.set_vars(
optdriver=4,
gwpara=2,
ecutwfn=ecut,
ecuteps=6.0,
ecutsigx=ecut,
symsigma=1,
gw_qprange=1,
)
return gs, nscf, scr, sigma
def make_inputs(tvars):
"""Constrcut the input files."""
structure = abidata.structure_from_ucell("GaAs")
multi = abilab.MultiDataset(structure, pseudos=abidata.pseudos("31ga.pspnc", "33as.pspnc"), ndtset=5)
# Global variables
kmesh = dict(ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[[0.5, 0.5, 0.5],
[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
global_vars = dict(ecut=2, paral_kgb=tvars.paral_kgb)
global_vars.update(kmesh)
multi.set_vars(global_vars)
# Dataset 1 (GS run)
multi[0].set_vars(
tolvrs=1e-6,
nband=4)
# NSCF run with large number of bands, and points in the the full BZ
multi[1].set_vars(
iscf=-2,
nband=20,
nstep=25,
kptopt=1,
tolwfr=1.e-8)
#kptopt=3)
# Fourth dataset: ddk response function along axis 1
# Fifth dataset: ddk response function along axis 2
# Sixth dataset: ddk response function along axis 3
for idir in range(3):
rfdir = 3 * [0]
rfdir[idir] = 1
multi[2+idir].set_vars(
iscf=-3,
nband=20,
nstep=1,
nline=0,
prtwf=3,
kptopt=3,
nqpt=1,
qpt=[0.0, 0.0, 0.0],
rfdir=rfdir,
rfelfd=2,
tolwfr=1.e-9,
)
# scf_inp, nscf_inp, ddk1, ddk2, ddk3
return multi.split_datasets()
def make_scf_nscf_bse_inputs(ngkpt=(6, 6, 6), ecut=6, ecuteps=3, mdf_epsinf=12.0, soenergy="0.8 eV"):
"""
Build and returns three `AbinitInput` objects to perform a
GS-SCF + GS-NSCF + BSE calculation with the model dielectric function.
Args:
ngkpt: Three integers giving the number of divisions for the k-mesh.
ecut: Cutoff energy for the wavefunctions.
ecuteps: Cutoff energy for the screened interation W_{GG'}.
mdf_epsinf: Static limit of the macroscopic dielectric functions.
Used to build the model dielectric function.
soenergy: Scissors operator energy (used to open the initial KS gap).
"""
multi = abilab.MultiDataset(
structure=abidata.structure_from_ucell("Si"), pseudos=abidata.pseudos("14si.pspnc"), ndtset=3
)
multi.set_mnemonics(True)
# Variables common to the three datasets.
multi.set_vars(ecut=ecut, nband=8, istwfk="*1", diemac=12.0)
# SCF run to get the density.
multi[0].set_vars(tolvrs=1e-8)
multi[0].set_kmesh(ngkpt=ngkpt, shiftk=(0, 0, 0))
# NSCF run on a randomly shifted k-mesh (improve the converge of optical properties)
multi[1].set_vars(iscf=-2, nband=15, tolwfr=1e-8, chksymbreak=0) # Skip the check on the k-mesh.
# This shift breaks the symmetry of the k-mesh.
multi[1].set_kmesh(ngkpt=ngkpt, shiftk=(0.11, 0.21, 0.31))
# BSE run with Haydock iterative method (only resonant + W + v)
multi[2].set_vars(
optdriver=99, # BS calculation
chksymbreak=0, # To skip the check on the k-mesh.
bs_calctype=1, # L0 is contstructed with KS orbitals and energies.
soenergy=soenergy, # Scissors operator used to correct the KS band structure.
bs_exchange_term=1, # Exchange term included.
bs_coulomb_term=21, # Coulomb term with model dielectric function.
mdf_epsinf=mdf_epsinf, # Parameter for the model dielectric function.
bs_coupling=0, # Tamm-Dancoff approximation.
bs_loband=2, # Lowest band included in the calculation
nband=6, # Highest band included in the calculation
bs_freq_mesh="0 6 0.02 eV", # Frequency mesh for the dielectric function
bs_algorithm=2, # Use Haydock method.
zcut="0.15 eV", # Complex shift to avoid divergences in the continued fraction.
ecutwfn=ecut, # Cutoff for the wavefunction.
ecuteps=ecuteps, # Cutoff for W and /bare v.
inclvkb=2, # The commutator for the optical limit is correctly evaluated.
)
# Same shift as the one used in the previous dataset.
multi[2].set_kmesh(ngkpt=ngkpt, shiftk=(0.11, 0.21, 0.31))
scf_input, nscf_input, bse_input = multi.split_datasets()
return scf_input, nscf_input, bse_input
def test_dfpt_methods(self):
"""Testing DFPT methods."""
gs_inp = AbinitInput(structure=abidata.structure_from_ucell("AlAs"),
pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"))
gs_inp.set_vars(
nband=4,
ecut=2,
ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid
0.0, 0.5, 0.0,
0.5, 0.0, 0.0,
0.5, 0.5, 0.5],
#shiftk=[0, 0, 0],
paral_kgb=1,
nstep=25,
tolvrs=1.0e-10,
)
################
# Phonon methods
################
with self.assertRaises(gs_inp.Error):
ddk_inputs = gs_inp.make_ddk_inputs(tolerance={"tolfoo": 1e10})
phg_inputs = gs_inp.make_ph_inputs_qpoint(qpt=(0, 0, 0), tolerance=None)
print("phonon inputs at Gamma\n", phg_inputs)
assert len(phg_inputs) == 2
assert np.all(phg_inputs[0]["rfatpol"] == [1, 1])
assert np.all(phg_inputs[1]["rfatpol"] == [2, 2])
assert all(np.all(inp["rfdir"] == [1, 0, 0] for inp in phg_inputs))
assert all(np.all(inp["kptopt"] == 2 for inp in phg_inputs))
if self.has_abinit():
# Validate
vs = phg_inputs.abivalidate()
assert all(v.retcode == 0 for v in vs)
#############
# DDK methods
#############
with self.assertRaises(gs_inp.Error):
ddk_inputs = gs_inp.make_ddk_inputs(tolerance={"tolvrs": 1e10})
ddk_inputs = gs_inp.make_ddk_inputs(tolerance=None)
print("DDK inputs\n", ddk_inputs)
assert len(ddk_inputs) == 3
assert all(inp["iscf"] == -3 for inp in ddk_inputs)
assert all(inp["rfelfd"] == 2 for inp in ddk_inputs)
if self.has_abinit():
# Validate
vs = ddk_inputs.abivalidate()
assert all(v.retcode == 0 for v in vs)
def make_inputs(ngkpt=(4,4,4), ecut=8, ecuteps=2):
"""
"""
inp = abilab.AbiInput(pseudos=abidata.pseudos("14si.pspnc"), ndtset=3)
#inp.set_structure(abidata.cif_file("si.cif"))
inp.set_structure(abidata.structure_from_ucell("Si"))
inp.set_variables(
ecut=ecut,
nband=8,
istwfk="*1",
diemac=12.0,
paral_kgb=1,
)
inp[1].set_variables(tolvrs=1e-8)
#inp[1].set_autokmesh(nksmall=min(ngkpt))
inp[1].set_kmesh(ngkpt=ngkpt, shiftk=(0, 0, 0))
inp[2].set_variables(
iscf=-2,
nband=15,
tolwfr=1e-8,
chksymbreak=0, # To skip the check on the k-mesh.
)
# This shift breaks the symmetry of the k-mesh.
inp[2].set_kmesh(ngkpt=ngkpt, shiftk=(0.11,0.21,0.31))
# BSE run with Haydock iterative method (only resonant + W + v)
inp[3].set_variables(
optdriver=99, # BS calculation
chksymbreak=0, # To skip the check on the k-mesh.
bs_calctype=1, # L0 is contstructed with KS orbitals and energies.
soenergy="0.8 eV", # Scissors operator used to correct the KS band structure.
bs_exchange_term=1, # Exchange term included.
bs_coulomb_term=21, # Coulomb term with model dielectric function.
mdf_epsinf=12.0, # Parameter for the model dielectric function.
bs_coupling=0, # Tamm-Dancoff approximation.
bs_loband=3,
nband=6,
#bs_freq_mesh=0 6 0.02 eV, # Frequency mesh.
bs_algorithm=2, # Haydock method.
#bs_haydock_niter=200 # Max number of iterations for the Haydock method.
#bs_haydock_tol=0.05 0, # Tolerance for the iterative method.
zcut="0.15 eV", # complex shift to avoid divergences in the continued fraction.
ecutwfn=ecut, # Cutoff for the wavefunction.
ecuteps=ecuteps, # Cutoff for W and /bare v used to calculate the BS matrix elements.
inclvkb=2, # The commutator for the optical limit is correctly evaluated.
)
inp[3].set_kmesh(ngkpt=ngkpt, shiftk=(0.11,0.21,0.31))
scf_input, nscf_input, bse_input = inp.split_datasets()
return scf_input, nscf_input, bse_input
def test_utils(self):
"""Test utilities for the generation of Abinit inputs."""
structure = data.structure_from_ucell("MgB2")
self.serialize_with_pickle(structure)
pseudos = data.pseudos("12mg.pspnc", "05b.soft_tm")
nval = structure.calc_nvalence(pseudos)
self.assertTrue(nval == 12)
shiftk = structure.calc_shiftk()
self.assert_equal(shiftk, [[0.0, 0.0, 0.5]])
def test_utils(self):
"""Test utilities for the generation of Abinit inputs."""
structure = data.structure_from_ucell("MgB2")
self.serialize_with_pickle(structure)
pseudos = data.pseudos("12mg.pspnc", "5b.pspnc")
nval = structure.num_valence_electrons(pseudos)
self.assertEqual(nval, 8)
shiftk = structure.calc_shiftk()
self.assert_equal(shiftk, [[0.0, 0.0, 0.5]])
def test_utils(self):
"""Test utilities for the generation of Abinit inputs."""
structure = data.structure_from_ucell("MgB2")
structure.abi_sanitize()
print(structure.abi_string)
self.serialize_with_pickle(structure)
pseudos = data.pseudos("12mg.pspnc", "5b.pspnc")
nval = structure.num_valence_electrons(pseudos)
self.assertEqual(nval, 8)
self.assert_equal(structure.calc_shiftk(), [[0.0, 0.0, 0.5]])
def build_flow(options):
"""
Create a `Flow` for phonon calculations:
1) One workflow for the GS run.
2) nqpt works for phonon calculations. Each work contains
nirred tasks where nirred is the number of irreducible phonon perturbations
for that particular q-point.
"""
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
if not options.workdir:
options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
flow = flowtk.Flow(workdir=options.workdir)
# This function constructs the input files for the phonon calculation:
# GS input + the input files for the phonon calculation.
pseudos = abidata.pseudos("14si.pspnc")
structure = abidata.structure_from_ucell("Si")
gs_inp = abilab.AbinitInput(structure, pseudos=pseudos)
# List of q-points for the phonon calculation.
#qpoints = np.reshape(qpoints, (-1, 3))
# Global variables used both for the GS and the DFPT run.
gs_inp.set_vars(
nband=4,
ecut=2.0,
ngkpt=[4, 4, 4],
nshiftk=4,
shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid
0.0, 0.5, 0.0,
0.5, 0.0, 0.0,
0.5, 0.5, 0.5],
#shiftk=[0, 0, 0],
paral_kgb=0,
diemac=12.0,
iomode=3,
tolvrs=1.0e-18,
)
# Get the qpoints in the IBZ. Note that here we use a q-mesh with ngkpt=(4,4,4) and shiftk=(0,0,0)
qpoints = gs_inp.abiget_ibz(ngkpt=(4, 4, 4), shiftk=(0, 0, 0)).points
# Build input for GS calculation and register the first work.
#work0 = flow.register_scf_task(scf_input)
#ph_work = flowtk.PhononWork.from_scf_task(work0[0], qpoints=qpoints, is_ngqpt=True)
#flow.register_work(ph_work)
ph_inputs = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=len(qpoints))
return flow
def relax_flow(workdir="tmp_sic_relax"):
manager = abilab.TaskManager.simple_mpi(mpi_ncpus=1)
flow = abilab.AbinitFlow(workdir, manager)
pseudos = data.pseudos("14si.pspnc", "6c.pspnc")
structure = data.structure_from_ucell("SiC")
global_vars = dict(
chksymbreak=0,
ecut = 20
)
ngkpt = [4,4,4]
shiftk = [[0.5,0.5,0.5],
[0.5,0.0,0.0],
[0.0,0.5,0.0],
[0.0,0.0,0.5]]
inp = abilab.AbiInput(pseudos=pseudos, ndtset=2)
inp.set_structure(structure)
inp.set_variables(**global_vars)
relax_inp, nscf_inp = inp[1:]
relax_inp.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
relax_inp.set_variables(
toldff=1e-6,
tolmxf=1e-5,
strfact=100,
ecutsm=0.5,
dilatmx=1.15,
ntime=100,
ionmov=2,
optcell=1,
)
nscf_inp.set_kpath(ndivsm=20)
nscf_inp.tolwfr = 1e-22
relax_inp, nscf_inp = inp.split_datasets()
# Initialize the workflow.
relax_task = flow.register_task(relax_inp, task_class=abilab.RelaxTask)
#work = RelaxWorkflow(self, ion_input, ioncell_input, workdir=None, manager=None):
nscf_task = flow.register_task(nscf_inp, deps={relax_task: "DEN"}, task_class=abilab.NscfTask)
return flow.allocate()
def scf_ph_inputs(tvars=None):
"""
This function constructs the input files for the phonon calculation:
GS input + the input files for the phonon calculation.
"""
# Crystalline AlAs: computation of the second derivative of the total energy
structure = abidata.structure_from_ucell("AlAs")
# List of q-points for the phonon calculation (4,4,4) mesh.
qpoints = [
0.00000000E+00, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 0.00000000E+00, 0.00000000E+00,
5.00000000E-01, 0.00000000E+00, 0.00000000E+00,
2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 2.50000000E-01, 0.00000000E+00,
-2.50000000E-01, 2.50000000E-01, 0.00000000E+00,
5.00000000E-01, 5.00000000E-01, 0.00000000E+00,
-2.50000000E-01, 5.00000000E-01, 2.50000000E-01,
]
qpoints = np.reshape(qpoints, (-1,3))
# Global variables used both for the GS and the DFPT run.
global_vars = dict(nband=4,
ecut=3.0,
ngkpt=[4, 4, 4],
shiftk=[0, 0, 0],
tolvrs=1.0e-6,
paral_kgb=0 if tvars is None else tvars.paral_kgb,
)
multi = abilab.MultiDataset(structure=structure, pseudos=abidata.pseudos("13al.981214.fhi", "33as.pspnc"),
ndtset=1+len(qpoints))
multi.set_vars(global_vars)
for i, qpt in enumerate(qpoints):
# Response-function calculation for phonons.
multi[i+1].set_vars(
nstep=20,
rfphon=1, # Will consider phonon-type perturbation
nqpt=1, # One wavevector is to be considered
qpt=qpt, # This wavevector is q=0 (Gamma)
kptopt=3,
)
#rfatpol 1 1 # Only the first atom is displaced
#rfdir 1 0 0 # Along the first reduced coordinate axis
#kptopt 2 # Automatic generation of k points, taking
# Split input into gs_inp and ph_inputs
return multi.split_datasets()
def build_flow(options):
# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
flow = flowtk.Flow(workdir, manager=options.manager, remove=options.remove)
pseudos = data.pseudos("14si.pspnc", "6c.pspnc")
structure = data.structure_from_ucell("SiC")
global_vars = dict(
chksymbreak=0,
ecut=20,
paral_kgb=0,
iomode=3,
)
ngkpt = [4, 4, 4]
shiftk = [[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]]
multi = abilab.MultiDataset(structure, pseudos=pseudos, ndtset=2)
multi.set_vars(global_vars)
relax_inp, nscf_inp = multi.split_datasets()
relax_inp.set_kmesh(ngkpt=ngkpt, shiftk=shiftk)
relax_inp.set_vars(
toldff=1e-6,
tolmxf=1e-5,
strfact=100,
ecutsm=0.5,
dilatmx=1.15,
ntime=100,
ionmov=2,
optcell=1,
)
nscf_inp.set_kpath(ndivsm=20)
nscf_inp.tolwfr = 1e-22
# Initialize the work.
relax_task = flow.register_task(relax_inp, task_class=flowtk.RelaxTask)
#work = RelaxWork(self, ion_input, ioncell_input, workdir=None, manager=None):
#nscf_task = flow.register_task(nscf_inp, deps={relax_task: "DEN"}, task_class=flowtk.NscfTask)
return flow
def test_utils(self):
"""Test utilities for the generation of Abinit inputs."""
structure = data.structure_from_ucell("MgB2")
structure.abi_sanitize()
structure.get_conventional_standard_structure()
print(structure.abi_string)
#print(structure._repr_html_())
self.serialize_with_pickle(structure)
pseudos = data.pseudos("12mg.pspnc", "5b.pspnc")
nval = structure.num_valence_electrons(pseudos)
self.assertEqual(nval, 8)
self.assert_equal(structure.calc_shiftk() , [[0.0, 0.0, 0.5]])
def setUp(self):
# Si ebands
si_structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
self.si_ebands = ebands_input(si_structure, abidata.pseudos("14si.pspnc"), ecut=2, kppa=10)
# Reference input string. Used to test if decorators do not change the initial Input.
self.si_ebands_inpstr = str(self.si_ebands)
# NiO bands with PAW
nio_structure = abidata.structure_from_ucell("NiO")
self.nio_ebands = ebands_input(nio_structure, abidata.pseudos("28ni.paw", "8o.2.paw"),
ecut=2, pawecutdg=4, kppa=10)
self.nio_ebands_inpstr = str(self.nio_ebands)
def test_input_errors(self):
"""Testing typical AbinitInput Error"""
si_structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
# Ambiguous list of pseudos.
with self.assertRaises(AbinitInput.Error):
AbinitInput(si_structure, pseudos=abidata.pseudos("14si.pspnc", "Si.oncvpsp"))
# Pseudos do not match structure.
with self.assertRaises(AbinitInput.Error):
AbinitInput(si_structure, pseudos=abidata.pseudos("13al.981214.fhi"))
# Negative triple product.
with self.assertRaises(AbinitInput.Error):
s = abidata.structure_from_ucell("Al-negative-volume")
AbinitInput(s, pseudos=abidata.pseudos("13al.981214.fhi"))
