def get_incar(self, structure):
incar = Incar()
if self.sort_structure:
structure = structure.get_sorted_structure()
comp = structure.composition
elements = sorted([el for el in comp.elements if comp[el] > 0],
key=lambda el: el.X)
most_electroneg = elements[-1].symbol
poscar = Poscar(structure)
for key, setting in self.incar_settings.items():
if key == "MAGMOM":
mag = []
for site in structure:
if hasattr(site, 'magmom'):
mag.append(site.magmom)
elif hasattr(site.specie, 'spin'):
mag.append(site.specie.spin)
elif str(site.specie) in setting:
mag.append(setting.get(str(site.specie)))
else:
mag.append(setting.get(site.specie.symbol, 0.6))
incar[key] = mag
elif key in ('LDAUU', 'LDAUJ', 'LDAUL'):
if most_electroneg in setting.keys():
incar[key] = [
setting[most_electroneg].get(sym, 0)
for sym in poscar.site_symbols
]
else:
incar[key] = [0] * len(poscar.site_symbols)
elif key == "EDIFF":
incar[key] = float(setting) * structure.num_sites
else:
incar[key] = setting
has_u = ("LDAUU" in incar and sum(incar['LDAUU']) > 0)
if has_u:
# modify LMAXMIX if LSDA+U and you have d or f electrons
# note that if the user explicitly sets LMAXMIX in settings it will
# override this logic.
if 'LMAXMIX' not in self.incar_settings.keys():
# contains f-electrons
if any([el.Z > 56 for el in structure.composition]):
incar['LMAXMIX'] = 6
# contains d-electrons
elif any([el.Z > 20 for el in structure.composition]):
incar['LMAXMIX'] = 4
else:
for key in incar.keys():
if key.startswith('LDAU'):
del incar[key]
if self.set_nupdown:
nupdown = sum([mag if mag > 0.6 else 0 for mag in incar['MAGMOM']])
incar['NUPDOWN'] = nupdown
return incar
def run_aconvasp_command(command, structure):
"""
Helper function for calling aconvasp with different arguments
"""
poscar = Poscar(structure)
p = subprocess.Popen(command,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE)
output = p.communicate(input=poscar.get_string())
return output
def test_str(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
#Silicon structure for testing.
latt = [[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
expected_str = '''Si2
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
Si
2
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 Si
'''
self.assertEquals(str(poscar), expected_str, "Wrong POSCAR output!")
#Vasp 4 type with symbols at the end.
poscar_string = """Test1
1.0
-3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 F
"""
expected = """Test1
1.0
3.840198 -0.000000 -0.000000
-1.920099 -3.325710 -0.000000
-0.000000 2.217138 -3.135509
Si F
1 1
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 F
"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(str(poscar), expected)
def plot_images(self, outfile):
"""
Generates a POSCAR with the calculated diffusion path with respect to the first endpoint.
:param outfile: Output file for the POSCAR
"""
sum_struct = self.__images[0].sites
for image in self.__images:
for site_i in self.__relax_sites:
sum_struct.append(
PeriodicSite(image.sites[site_i].specie,
image.sites[site_i].frac_coords,
self.__images[0].lattice,
to_unit_cell=True,
coords_are_cartesian=False))
sum_struct = Structure.from_sites(sum_struct, validate_proximity=False)
p = Poscar(sum_struct)
p.write_file(outfile)
def test_str(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
#Silicon structure for testing.
latt = [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
expected_str = '''Si2
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
Si
2
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 Si'''
self.assertEquals(str(poscar), expected_str, "Wrong POSCAR output!")
def test_velocities(self):
si = 14
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
#Silicon structure for testing.
latt = [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]
struct = Structure(latt, [si, si], coords)
poscar = Poscar(struct)
poscar.set_temperature(900)
v = np.array(poscar.velocities)
for x in np.sum(v, axis=0):
self.assertAlmostEqual(
x, 0, 7, 'Velocities initialized with a net momentum')
temperature = struct[0].specie.atomic_mass * AMU_TO_KG * \
np.sum(v ** 2) / (3 * BOLTZMANN_CONST) * 1e10
self.assertAlmostEqual(temperature, 900, 4,
'Temperature instantiated incorrectly')
def get_new_poscar_lines(self):
"""
Pymatgen does not realize that decorated elements (species) should be
treated as different sites in VASP.
This routine hacks the poscar file (which has already been hacked to go from 5.x to 4.6)
to include the correct number of distinct sites.
"""
self.check_structure_is_modified()
# get a poscar consistent with the internally modified structure
poscar = Poscar(self.structure)
lines = poscar.get_string(vasp4_compatible=True).split('\n')
hack_line = ''
for element, number in self.species_dict.items():
hack_line += ' %i'%number
lines[5] = hack_line
return lines
def look4VacantPosition():
""" """
s = mg.Structure.from_file(sys.argv[1])
fill_s = s.copy()
grid = mg.Structure(s.lattice, [], [])
# grid step in frac coords
step = 0.1
# radius for looking for neighbors
radius = 2.5
# threshold to exclude vacant position
els = s.composition.elements
th = {els[0]: 1.7, els[1]: 2., els[2]: 2.}
# grid ranges
xmin = 0
xmax = 1
ymin = 0
ymax = 1
zmin = 0
zmax = 1
print("Parameters\n" + 10 * "-")
print("Grid step : %6.2f" % step)
print("Neighbors radius : %6.2f" % radius)
print("threshold tolerence:")
for el, dmax in th.items():
print("X - %2s : %8.3f" % (el.symbol, dmax))
vaclist = list()
for xi in np.arange(xmin, xmax, step):
for yi in np.arange(ymin, ymax, step):
for zi in np.arange(zmin, zmax, step):
vacsite = mg.PeriodicSite("X", [xi, yi, zi], s.lattice)
neigh = s.get_neighbors(vacsite, radius)
grid.append("X", [xi, yi, zi])
add = True
nLi = 0
for neighsite, d in neigh:
dmax = th[neighsite.specie]
if d < dmax:
add = False
break
if neighsite.specie.symbol == "Li":
nLi += 1
if nLi >= 2:
print("nLi >= 2")
add = False
if add:
fill_s.append(vacsite.specie, vacsite.frac_coords)
vaclist.append([xi, yi, zi])
print("\nResults\n" + 7 * "-")
print(
"Write file 'POSCAR_fill.vasp': initial structure + vacant positions")
Poscar(fill_s).write_file("POSCAR_fill.vasp")
print("Write file 'POSCAR_grid.vasp': grid positions (%d atoms)" %
len(grid))
Poscar(grid).write_file("POSCAR_grid.vasp")
print("\nNumber of positions : %d" % len(vaclist))
if len(vaclist) < 30:
for xyz in vaclist:
print((3 * "%8.3f") % tuple(xyz))
#separate slab
iface_slab = iface.slab
iface_slab.sort()
#set selective dynamics flags as required
true_site= [1, 1, 1]
false_site= [0, 0, 0]
sd_flag_iface= []
j= 0
sd_flag_slab= []
for i in iface.sites:
sd_flag_iface.append(false_site)
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
#POSCAR and POTCAR construction, pending setting of exact flags for POSCAR
interface_poscar = Poscar(iface, selective_dynamics= sd_flag_iface)
interface_potcar= Potcar(interface_poscar.site_symbols)
slab_poscar = Poscar(iface_slab, selective_dynamics= sd_flag_slab)
slab_potcar= Potcar(slab_poscar.site_symbols)
#write the files in appropriate directories
interface_poscar.write_file("./Interface/POSCAR_PbS100DMF_interface_with_sd.vasp")
slab_poscar.write_file("./Slab/POSCAR_PbS100_slab_with_sd.vasp")
interface_potcar.write_file("./Interface_with_vdw/POTCAR")
slab_potcar.write_file("./Slab_with_vdw/POTCAR")
#set the common INCAR file and KPOINTS
incar_dict = {
'SYSTEM': 'ligand_PbS',
'ENCUT': 600,
'ISIF': 2,
def get_poscar(self, structure):
"""
Returns Poscar from a structure.
"""
return Poscar(structure)
def get_VASP_inputs(structure, workdir, job_name, nproc=64, kppa=500, extra_incar_dict = None):
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
poscar = Poscar(structure)
list_potcar_singles, potcar= get_POTCAR(poscar)
kpoints = Kpoints.automatic_density(structure, kppa=kppa)
# Default values
incar_dict = dict( SYSTEM = structure.formula, # Name of job
LREAL = 'Auto', # Should projections be done in real space? Let VASP decide
ENCUT = 520., # 520. eV, just like Ceder
IBRION = 2, # Controls ionic relataxion: 1-> DISS, 2 -> CG, 3-> MD
EDIFF = 1E-7, # criterion to stop SCF loop, in eV
EDIFFG = -1E-3, # criterion to stop ionic relaxations. Negative means FORCES < |EDIFFG|
PREC = 'HIGH', # level of precision
AMIX = 0.2,
AMIX_MAG= 0.8,
BMIX = 0.001,
BMIX_MAG= 0.001,
NSW = 150, # Maximum number of ionic steps
ISMEAR = 0, # smearing scheme. Use 0 for insulators, as suggested by VASPWIKI
ISPIN = 2, # spin polarized
NPAR = 8, # VASPWIKI recommends sqrt(ncore)
LSCALU = False, # Don't use scalapack. Probably a can of worms.
ALGO = 'NORMAL', # what ionic relaxation scheme to use?
LORBIT = 11, # 11 prints out the DOS
ISIF = 3, # Controls the computation of stress tensor. 3 computes everything
NSIM = 4, # how many bands to treat in parallel? Default is 4, probably fine.
SIGMA = 0.025, # smearing in eV
LMAXMIX = 4, # Description: LMAXMIX controls up to which l-quantum number the one-center PAW charge densities are passed through the charge density mixer. MaterialsProject uses 4.
LCHARG = False, # Write charge densities?
LWAVE = False, # write out the wavefunctions?
LPLANE = True, # Plane distribution of FFT coefficients. Reduces communications in FFT.
NELM = 100, # maximum number of SCF cycles.
NELMDL = -10, # since initial orbitals may be random, fixes hamiltonian for |NELM| SCF cycles to give wf a chance to simmer down.
ISTART = 0, # begin from scratch!
ISYM = 2) # use symmetry
if extra_incar_dict != None:
incar_dict.update( extra_incar_dict )
incar = Incar.from_dict(incar_dict )
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
potcar.sort()
hack_potcar_file(workdir,list_potcar_singles)
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def get_poscar(self, structure):
sym_finder = SymmetryFinder(structure, symprec=0.01)
return Poscar(sym_finder.get_primitive_standard_structure())
def get_poscar(self, structure):
if self.sort_structure:
structure = structure.get_sorted_structure()
return Poscar(structure)
def get_poscar(self, structure):
return Poscar(structure)
def get_calibration_task(structure, phase="CalibrateBulk", \
slab_interface_params={'hkl':[1,0,0], 'ligand': None},\
turn_knobs={}, incar_params={}, other_params={}):
"""
returns general calibration task for a structure
Args:
structure : pymatgen structure to be calibrated (can be a bulk, ligand, slab
or interface)
phase : calibration type, viz. CalibrateBulk, CalibrateMolecule,
CalibrateSlab, CalibrateInterface
hkl : in case of Slab and Interface miller indices of facet
turn_knobs : specifies the parameters to be calibrated
incar_params : dictionary of additional incar parameters, refer defined
incar_dict for defaults
other_params : other parameters for calibration, viz. job_dir, is_matrix, etc.
described in the calibrate module
"""
#structure definition
poscar = Poscar(structure)
incar_dict = {
'SYSTEM': 'slab',
'ENCUT': 500,
'ISIF': 2,
'IBRION': 2,
'ISMEAR': 1,
'EDIFF': 1e-05,
'NPAR': 4,
'SIGMA': 0.1,
'PREC': 'Accurate'
}
if incar_params:
incar_dict.update(incar_params)
incar = Incar.from_dict(incar_dict)
kpoints = Kpoints.monkhorst_automatic(kpts=(8, 8, 1))
que = {
'nnodes': 1,
'nprocs': 16,
'walltime': '48:00:00',
'job_bin': '/home/km468/Software/VASP/vaspsol_kappa.5.3.5/vasp'
}
# calibration task: relax hkl
calparams = {}
calparams['calibrate'] = phase
calparams['incar'] = incar.as_dict()
calparams['poscar'] = poscar.as_dict()
calparams['kpoints'] = kpoints.as_dict()
calparams['que_params'] = que
calparams['turn_knobs'] = turn_knobs
if phase == 'CalibrateSlab':
calparams['system'] = {
'hkl': slab_interface_params['hkl'],
'ligand': slab_interface_params['ligand']
}
elif phase == 'CalibrateInterface':
calparams['system'] = {
'hkl': hkl,
'ligand': structure.ligand.reduced_formula
}
calparams['other_params'] = {
'is_matrix': False,
'from_ase': True,
'Grid_type': 'M'
}
if other_params:
calparams['other_params'].update(other_params)
return MPINTCalibrateTask(calparams)
