def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst)
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, Kpoints.supported_modes.Automatic)
self.assertEqual(kpoints.kpts, [[100]])
filepath = self.TEST_FILES_DIR / 'POSCAR'
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[1, 3, 3]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 10, 13]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.from_string("""k-point mesh
0
G
10 10 10
0.5 0.5 0.5
""")
self.assertArrayAlmostEqual(kpoints.kpts_shift, [0.5, 0.5, 0.5])
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Monkhorst)
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, Kpoints.supported_modes.Automatic)
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[1, 3, 3]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 10, 13]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, Kpoints.supported_modes.Gamma)
kpoints = Kpoints.from_string("""k-point mesh
0
G
10 10 10
0.5 0.5 0.5
""")
self.assertArrayAlmostEqual(kpoints.kpts_shift, [0.5, 0.5, 0.5])
def generate_3Dkpoints(struct,dirname):
#print(" input the dimensionality and mesh grid density ")
tip='''
Accuracy Levels: (1) Low: 0.04~0.03;
(2) Medium: 0.03~0.02;
(2) Fine: 0.02~0.01;
'''
warn_tip(1,tip)
print("Input KP-Resolved Value (unit: 2*PI/Ang):")
wait_sep()
in_str=""
while in_str=="":
in_str=input().strip()
delta_k=float(in_str)
(lka,lkb,lkc)=struct.lattice.reciprocal_lattice.abc
ka=ceil(lka/(2*np.pi)/delta_k)
kb=ceil(lkb/(2*np.pi)/delta_k)
ka_dis=np.linspace(-0.5,0.5,ka)
kb_dis=np.linspace(-0.5,0.5,kb)
kxx,kyy=np.meshgrid(ka_dis,kb_dis)
kpts=[[i[0], i[1], 0.0] for i in zip(kxx.flat,kyy.flat)]
tmp_K="3D K-meshs by maptool with : "+ str(ka)+"x"+ str(kb)+ "\n 1\nReciprocal\n 0 0 0 1"
# initialize a Kpionts instance from template string
reciprocal_kpoints=Kpoints.from_string(tmp_K)
reciprocal_kpoints.labels=None
reciprocal_kpoints.kpts=kpts
reciprocal_kpoints.num_kpts=ka*kb
reciprocal_kpoints.kpts_weights=[1.0]*(ka*kb)
reciprocal_kpoints.write_file(os.path.join(dirname, "KPOINTS"))
def get_kpoints(
structure,
min_distance=0,
min_total_kpoints=1,
kppra=None,
gap_distance=7,
remove_symmetry=None,
include_gamma="auto",
header="simple",
incar=None,
):
"""
Get kpoints object from JHU servlet, per Wisesa-McGill-Mueller
methodology. Refer to http://muellergroup.jhu.edu/K-Points.html
and P. Wisesa, K. A. McGill, T. Mueller, Phys. Rev. B 93,
155109 (2016)
Args:
structure (Structure): structure object
min_distance (float): The minimum allowed distance
between lattice points on the real-space superlattice
min_total_kpoints (int): The minimum allowed number of
total k-points in the Brillouin zone.
kppra (float): minimum k-points per reciprocal atom.
gap_distance (float): auto-detection threshold for
non-periodicity (in slabs, nanowires, etc.)
remove_symmetry (string): optional flag to control
symmetry options, can be none, structural,
time_reversal, or all
include_gamma (string or bool): whether to include
gamma point
header (string): "verbose" or "simple", denotes
the verbosity of the header
incar (Incar): incar object to upload
"""
config = locals()
config.pop("structure", "incar")
# Generate PRECALC string
precalc = "".join([f"{k}={v}\n" for k, v in config.items()])
precalc = precalc.replace("_", "").upper()
precalc = precalc.replace("REMOVESYMMETRY", "REMOVE_SYMMETRY")
precalc = precalc.replace("TIMEREVERSAL", "TIME_REVERSAL")
url = "http://muellergroup.jhu.edu:8080/PreCalcServer/PreCalcServlet"
temp_dir_name = tempfile.mkdtemp()
cwd = os.getcwd()
os.chdir(temp_dir_name)
with open("PRECALC",
"w+") as precalc_file, open("POSCAR", "w+") as poscar_file, open(
"INCAR", "w+") as incar_file:
precalc_file.write(precalc)
poscar_file.write(structure.to("POSCAR"))
files = [("fileupload", precalc_file), ("fileupload", poscar_file)]
if incar:
incar_file.write(incar.get_string())
files.append(("fileupload", incar_file))
precalc_file.seek(0)
poscar_file.seek(0)
incar_file.seek(0)
r = requests.post(url, files=files)
kpoints = Kpoints.from_string(r.text)
os.chdir(cwd)
shutil.rmtree(temp_dir_name)
return kpoints
def get_kpoints(structure, min_distance=0, min_total_kpoints=1,
kppra=None, gap_distance=7, remove_symmetry=None,
include_gamma="auto", header="simple", incar=None):
"""
Get kpoints object from JHU servlet, per Wisesa-McGill-Mueller
methodology. Refer to http://muellergroup.jhu.edu/K-Points.html
and P. Wisesa, K. A. McGill, T. Mueller, Phys. Rev. B 93,
155109 (2016)
Args:
structure (Structure): structure object
min_distance (float): The minimum allowed distance
between lattice points on the real-space superlattice
min_total_kpoints (int): The minimum allowed number of
total k-points in the Brillouin zone.
kppra (float): minimum k-points per reciprocal atom.
gap_distance (float): auto-detection threshold for
non-periodicity (in slabs, nanowires, etc.)
remove_symmetry (string): optional flag to control
symmetry options, can be none, structural,
time_reversal, or all
include_gamma (string or bool): whether to include
gamma point
header (string): "verbose" or "simple", denotes
the verbosity of the header
incar (Incar): incar object to upload
"""
config = locals()
config.pop("structure", "incar")
# Generate PRECALC string
precalc = ''.join(["{}={}\n".format(k, v) for k, v in config.items()])
precalc = precalc.replace('_', '').upper()
precalc = precalc.replace('REMOVESYMMETRY', 'REMOVE_SYMMETRY')
precalc = precalc.replace('TIMEREVERSAL', 'TIME_REVERSAL')
url = "http://muellergroup.jhu.edu:8080/PreCalcServer/PreCalcServlet"
temp_dir_name = tempfile.mkdtemp()
cwd = os.getcwd()
os.chdir(temp_dir_name)
precalc_file = open("PRECALC", 'w+')
poscar_file = open("POSCAR", 'w+')
incar_file = open("INCAR", 'w+')
precalc_file.write(precalc)
poscar_file.write(structure.to("POSCAR"))
files = [("fileupload", precalc_file),
("fileupload", poscar_file)]
if incar:
incar_file.write(incar.get_string())
files.append(("fileupload", incar_file))
precalc_file.seek(0)
poscar_file.seek(0)
incar_file.seek(0)
r = requests.post(url, files=files)
precalc_file.close()
poscar_file.close()
incar_file.close()
kpoints = Kpoints.from_string(r.text)
os.chdir(cwd)
shutil.rmtree(temp_dir_name)
return kpoints
