def NaWat3_linear_geom(x):
# hf/aug-cc-pvdz optimized (H2O)_3Na+ cluster (higher-E stationary pt)
# excursion of leftmost water in the O -- Na - OH - O configuration
origin = [['Na', np.array([0.21087905, -1.07845876, -0.00384438])],
['O', np.array([-0.70376204, 3.26354462, -0.00020967])],
['H', np.array([-0.97394692, 3.75994642, -0.75799166])],
['H', np.array([-0.97895278, 3.76348016, 0.75329091])],
['O', np.array([-0.44282906, -3.23885333, 0.00243490])],
['H', np.array([-0.60917435, -3.78448428, 0.75766465])],
['H', np.array([-0.59937587, -3.79222625, -0.74928940])],
['O', np.array([0.97598687, 0.99264382, 0.00069382])],
['H', np.array([0.42857199, 1.77680728, 0.00287819])],
['H', np.array([1.87069029, 1.29765224, 0.00193479])]]
r_na = origin[0][1]
r_o = origin[4][1]
line = r_o - r_na
line = line / np.linalg.norm(line)
origin[4][1] += x * line
origin[5][1] += x * line
origin[6][1] += x * line
g = []
for atom in origin:
g.append([atom[0]])
g[-1].extend(list(atom[1]))
# recommend scanning np.linspace(-0.2, 1.0, 11)
geom.load_geometry(g)
def NaWat3_triangle_geom(x):
# hf/aug-cc-pvdz optimized (H2O)_3Na+ cluster (lower-E stationary pt)
# excursion of Na atom normal to the O-O-O plane
origin = '''Na -0.00000166 0.00006962 0.00049518
O -1.51025934 1.71557888 0.00059985
H -1.44772201 2.53265513 0.47371767
H -2.32859634 1.75777493 -0.47258270
O 2.24074836 0.45075145 0.00029807
H 2.68652258 1.13571663 -0.47663878
H 2.91681988 -0.00819915 0.47744007
O -0.72998035 -2.16575869 0.00084616
H -1.47070339 -2.51998088 0.47117176
H -0.35442799 -2.89606213 -0.46923496'''.split('\n')
assert len(origin) == 10
for i in range(10):
at = origin[i].split()
name = at[0]
pos = np.array(map(float, at[1:4]))
origin[i] = [name, pos]
vec1 = origin[1][1] - origin[4][1]
vec2 = origin[1][1] - origin[7][1]
scan_vec = np.cross(vec1, vec2)
scan_vec /= np.linalg.norm(scan_vec)
origin[0][1] += x * scan_vec
g = []
for atom in origin:
g.append([atom[0]])
g[-1].extend(list(atom[1]))
# scan np.linspace(-1.5, 1.5, 13)
geom.load_geometry(g)
def He3_dimerize_geom(x):
# x sweeps from 0 to 1
# coordinate scans from one uhf/avdz local min to another
# spin density goes (.25|.5|.25) --> (.5|.5|0)
g = [['He', -1.24 + x * (-1.07825455 + 1.24), 0.0, 0.0],
['He', 0.0, 0.0, 0.0],
['He', 1.24 + x * (1.96169068 - 1.24), 0.0, 0.0]]
geom.load_geometry(g)
def He8_geom(ring_pos, radius=2.385, nsolvent=5):
g = [['He', -1.074, 0.0, 0.0], ['He', 0.0, 0.0, 0.0],
['He', 1.986, 0.0, 0.0]]
dangle = 2 * np.pi / nsolvent
angles = [n * dangle for n in range(nsolvent)]
for angle in angles:
g.append([
'He', ring_pos,
round(radius * np.cos(angle), 3),
round(radius * np.sin(angle), 3)
])
geom.load_geometry(g)
def parse_input(input_file):
'''Open input_file, parse it, load geometry, and MPI-broadcast the data'''
if MPI.rank == 0:
with open(input_file) as fp:
params.parse(fp)
geom.load_geometry(params.options['geometry'])
params.options = MPI.bcast(params.options, master=0)
geom.geometry = MPI.bcast(geom.geometry, master=0)
lattice.lattice = MPI.bcast(lattice.lattice, master=0)
lattice.lat_vecs = MPI.bcast(lattice.lat_vecs, master=0)
lattice.lat_vecs_inv = MPI.bcast(lattice.lat_vecs_inv, master=0)
lattice.PBC_flag = MPI.bcast(lattice.PBC_flag, master=0)
def Ar4_symm_geom(x):
g = [['Ar', 0.0, 0.0, 0.0], ['Ar', x, 0.0, 0.0], ['Ar', 2 * x, 0.0, 0.0],
['Ar', 3 * x, 0.0, 0.0]]
geom.load_geometry(g)
def Ar4_geom(x):
# about minimum at UHF/LANL2DZ ECP
g = [['Ar', 0.0 + x, 0.0, 0.0], ['Ar', 3.467, 0.0, 0.0],
['Ar', 6.061, 0.0, 0.0], ['Ar', 9.528 - x, 0.0, 0.0]]
geom.load_geometry(g)
def He4_asymm_geom(x):
g = [['He', -2.5 + (-2.06 + 2.5) * x, 0.0, 0.0],
['He', -0.54 + (-.98 + .54) * x, 0.0, 0.0],
['He', 0.54 + (0.98 - 0.54) * x, 0.0, 0.0],
['He', 2.5 + (2.06 - 2.5) * x, 0.0, 0.0]]
geom.load_geometry(g)
def He4_symm_geom(x):
g = [['He', 0.0, 0.0, 0.0], ['He', x, 0.0, 0.0], ['He', 2 * x, 0.0, 0.0],
['He', 3 * x, 0.0, 0.0]]
geom.load_geometry(g)
def He3_excursion_geom(x):
# x is displacement of weakly bound He from the dimer cation
# x == 0 is minimum at uhf/avdz
g = [['He', -1.07825455, 0.0, 0.0], ['He', 0.0, 0.0, 0.0],
['He', 1.96169068 + x, 0.0, 0.0]]
geom.load_geometry(g)
def He2_geom(x):
g = [['He', 0.0, 0.0, 0.0], ['He', x, 0.0, 0.0]]
geom.load_geometry(g)
help='points per dimension in rectangular k-grid before truncation')
parser.add_argument('--smooth',
action='store_true',
help='force acoustic branches to zero at gamma point')
parser.add_argument('--binary_file',
type=str,
help='save freqs as binary numpy array')
args = parser.parse_args()
return args
if __name__ == "__main__":
args = parseargs()
#geom.load_geometry(open(args.structure).read().replace('H','D'))
geom.load_geometry(args.structure)
if args.bz_file:
bz = np.loadtxt(args.bz_file)
assert bz.shape[1] == 3 and len(bz.shape) == 2
print "# Loaded %d kpoints from file" % len(bz)
else:
bz = make_brillouin_zone3D(args.kmesh_density)
print "# Generated %d kpoints in 1st BZ" % len(bz)
if args.bz_only:
for kvec in bz:
print kvec[0], kvec[1], kvec[2]
sys.exit(0)
if args.hessian is None: