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:
if os.getenv("READTHEDOCS", False):
__file__ = os.path.join(os.getcwd(), "run_phfrozen_ebands.py")
options.workdir = os.path.basename(__file__).replace(
".py", "").replace("run_", "flow_")
# build the structures
base_structure = abilab.Structure.from_file(data.cif_file("si.cif"))
modifier = abilab.StructureModifier(base_structure)
etas = [-0.1, 0, +0.1]
ph_displ = np.reshape(np.zeros(3 * len(base_structure)), (-1, 3))
ph_displ[0, :] = [+1, 0, 0]
ph_displ[1, :] = [-1, 0, 0]
displaced_structures = modifier.displace(ph_displ, etas, frac_coords=False)
flow = flowtk.Flow(options.workdir, manager=options.manager)
for structure in displaced_structures:
# Create the work for the band structure calculation.
scf_input, nscf_input = make_scf_nscf_inputs(structure)
work = flowtk.BandStructureWork(scf_input, nscf_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_")
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 raman_flow():
# Get the unperturbed structure.
base_structure = abilab.Structure.from_abivars(unit_cell)
pseudos = ["14si.pspnc"]
workdir = os.path.join(os.path.dirname(__file__), "test_abipy_new")
manager = abilab.TaskManager.from_user_config()
#manager = abilab.TaskManager.from_file("bfo_manager.yml")
policy = TaskPolicy(autoparal=0)
gs_manager = manager.deepcopy()
# Initialize flow. Each workflow in the flow defines a complete BSE calculation for given eta.
flow = abilab.Flow(workdir, manager)
# There will be kppa/natom kpoints in the unit cell !
kppa = 3456 # ngkpt = [12,12,12] for the primitive cell
kppa_gs = 1728 # ngkpt = [8,8,8] for the primitive cell
etas = [-1, 0, 1] # Anyway, it rescales everything at the end :-)
eta = 0.01
scale_matrix = [[-1, 0, 1], [-1, 1, 0], [-1, -1, 0]]
ph_tot = np.array([[0.01, 0.011, 0.021], [-0.01, 0.041, -0.02]])
modifier = abilab.StructureModifier(base_structure)
displaced_structure = modifier.frozen_phonon([0.5, 0.5, 0.5],
ph_tot,
do_real=True,
frac_coords=False,
scale_matrix=scale_matrix)
structure = displaced_structure
ksampgs = KSampling.automatic_density(structure,
kppa_gs,
chksymbreak=0,
shifts=[0, 0, 0])
gs_inp = gs_input(structure, pseudos, ksampgs)
wflow = abilab.Work()
gs_t = wflow.register_scf_task(gs_inp)
gs_t.set_manager(gs_manager)
flow.register_work(wflow, workdir="gs_task")
ksamp = KSampling.automatic_density(structure,
kppa,
chksymbreak=0,
shifts=[1 / 4, 1 / 4, 1 / 4])
flow.register_work(raman_workflow(structure, pseudos, gs_t, ksamp),
workdir="bse_task")
return flow.allocate()
def raman_flow(options):
# Get the unperturbed structure.
pseudos = data.pseudos("14si.pspnc")
base_structure = data.structure_from_ucell("Si")
ngkpt = [6, 6, 6]
etas = [-.002, -.001, 0, +.001, +.002]
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)
# Initialize flow. Each workflow in the flow defines a complete BSE calculation for given eta.
workdir = options.workdir
if not options.workdir:
workdir = os.path.basename(__file__).replace(".py", "").replace(
"run_", "flow_")
#workdir = os.path.join(os.path.dirname(__file__), base_structure.formula.replace(" ","") + "_RAMAN")
manager = options.manager
shell_manager = manager.to_shell_manager(mpi_procs=1)
ddk_manager = manager.deepcopy()
flow = abilab.Flow(workdir, manager=manager)
# Generate the different shifts to average
ndiv = 1
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]
for structure, eta in zip(displaced_structures, etas):
for ishift, shift in enumerate(all_shifts):
flow.register_work(raman_work(structure, pseudos, ngkpt, shift,
ddk_manager, shell_manager),
workdir="eta_" + str(eta) + "shift_" +
str(ishift))
return flow
