def internals(fn, save=None):
with open(fn) as handle:
mol = load(handle, fmt="xyz")
ic = InternalCoords(mol)
B_mat = ic.B_matrix(mol)
print(B_mat)
if save:
fmt = "% 1.4f"
np.savetxt(save, B_mat, fmt=fmt)
def get_berny(args):
geom = geomlib.load(sys.stdin, args.format)
if args.paramfile:
with open(args.paramfile) as f:
params = json.load(f)
else:
params = None
berny = Berny(geom, **params)
next(berny)
return berny
def get_berny(args):
geom = geomlib.load(sys.stdin, args.format)
if args.paramfile:
with open(args.paramfile) as f:
params = json.load(f)
else:
params = None
berny = Berny(geom, **params)
next(berny)
return berny
#!/usr/bin/env
import numpy as np
from berny.geomlib import load
from berny.coords import InternalCoords
np.set_printoptions(suppress=True, precision=4)
fn = "/scratch/programme/pysisyphus/xyz_files/h2o.xyz"
with open(fn) as handle:
mol = load(handle, fmt="xyz")
ic = InternalCoords(mol)
print(mol)
print(ic)
bmat = ic.B_matrix(mol)
print(bmat)
def internals(fn, save=None):
with open(fn) as handle:
mol = load(handle, fmt="xyz")
ic = InternalCoords(mol)
B_mat = ic.B_matrix(mol)
print(B_mat)
if save:
fmt = "% 1.4f"
np.savetxt(save, B_mat, fmt=fmt)
# H2O2
h2o2_fn = "/scratch/programme/pysisyphus/xyz_files/h2o2_hf_321g_opt.xyz"